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The history of Islam in southern Italy began with the first Muslim settlement in Sicily, at Mazara, which was occupied in 827. The subsequent rule of Sicily and Malta started in the 10th century. Islamic rule over Sicily began in 902, and the Emirate of Sicily lasted from 965 until 1061. Though Sicily was the primary Muslim stronghold in Italy, some temporary footholds, the most substantial of which was the port city of Bari (occupied from 847 until 871), were established on the mainland peninsula, with Muslim raids reaching as far north as Rome and Piedmont. The Muslim raids were part of a larger struggle for power in Italy and Europe, with Christian Byzantine, Frankish, Norman and local Italian forces also competing for control. Muslims were sometimes sought as allies by various Christian factions against other factions.
The first permanent Arab settlement on Sicily occurred in 827, but it was not until Taormina fell in 902 that the entire island fell under their sway, though Rometta held out until 965. In that year the Kalbids established the independence of their emirate from the Fatimid caliphate. In 1061 the first Norman conquerors took Messina, and by 1071 Palermo and its citadel (1072) were captured. In 1091 Noto fell to the Normans, and the conquest was complete. Malta fell later that year, though the Arab administration was kept in place, marking the final chapter of this period. The conquests of the Normans established Roman Catholicism firmly in the region, where Eastern Christianity had been prominent during the time of Byzantine rule and even remained significant during Islamic period. Widespread conversion ensued, leading to the disappearance of Islam in Sicily by the 1280s. The Muslim Ottoman Empire later attempted to gain a foothold in Italy with little success. In 1245, Muslim Sicilians were deported to the settlement of Lucera, by order of Holy Roman Emperor Frederick II. In 1300, Giovanni Pipino di Barletta, count of Altamura, seized Lucera and exiled or sold into slavery its population, bringing an end to the medieval Muslim presence in Italy.
The first attacks of Islamic ships on Sicily, then part of the Eastern Roman Empire, occurred in 652. These were Arab Mujahideen directed by the Caliph of Syria, Muawiyah I, and led by Mu'àuia ibn-Hodeig (Mu`āwiyah ibn Hudayj) of the Kindah tribe, and they remained on the island for several years. Olympius, the Byzantine exarch of Ravenna, came to Sicily to oust the invaders but failed. Soon after, the Arabs returned to Syria after collecting a sufficiently large amount of booty.
A second Arab expedition to Sicily occurred in 669. This time, a strong, ravaging force consisting of 200 ships from Alexandria attacked the island. They sacked Syracuse and returned to Egypt after a month of pillaging. After the Umayyad conquest of Africa (completed around 700), attacks from Muslim fleets repeated in 703, 728, 729, 730, 731, 733, and 734. The last two Arab assaults were met with substantial Byzantine resistance.
The first true conquest expedition was launched in 740. In that year, Habib ibn Abi Obeida al-Fihri, who had participated in the 728 attack, successfully captured Syracuse. Though ready to conquer the whole island, the expedition was forced to return to Tunisia by a Berber revolt. A second attack in 752 aimed only to sack Syracuse again.
In 805, the imperial patrician of Sicily, Constantine, signed a ten-year truce with Ibrahim I ibn al-Aghlab, Emir of Ifriqiya, but this did not prevent Muslim fleets from other areas of Africa and Spain from attacking Sardinia and Corsica from 806–821. In 812, Ibrahim's son, Abdallah I, sent an invasion force to conquer Sicily. His ships were first harassed by the intervention of Gaeta and Amalfi and were later destroyed in great number by a tempest. However, they managed to conquer the island of Lampedusa and to ravage Ponza and Ischia in the Tyrrhenian Sea. A further agreement between the new patrician Gregorius and the emir established the freedom of commerce between southern Italy and Ifriqiya. After a further attack in 819 by Mohammed ibn-Adballad, cousin of Emir Ziyadat Allah I, no subsequent Muslim attacks on Sicily are mentioned by sources until 827.
The Muslim conquest of Sicily and parts of southern Italy lasted 75 years. According to some sources, the conquest was spurred by Euphemius, a Byzantine commander who feared punishment by Emperor Michael II for a sexual indiscretion. After a short-lived conquest of Syracuse, he was proclaimed emperor but was compelled by loyal forces to flee to the court of Ziyadat Allah in Africa. The latter agreed to conquer Sicily, with the promise to leave it to Euphemius in exchange for a yearly tribute. He entrusted its conquest to the 70 year-old qadi, Asad ibn al-Furat. The Muslim force numbered 10,000 infantry, 700 cavalry, and 100 ships, reinforced by the fleet of Euphemius and, after the landing at Mazara del Vallo, by knights. The first battle against Byzantine troops occurred on July 15, 827, near Mazara, resulting in an Aghlabid victory.
Asad subsequently conquered the southern shore of the island and laid siege to Syracuse. After a year of siege and an attempted mutiny, his troops were able to defeat a large army sent from Palermo backed by a Venetian fleet led by doge Giustiniano Participazio. However, the Muslims retreated to the castle of Mineo when a plague killed many of their troops and Asad himself. They later returned to the offensive but failed to conquer Castrogiovanni (the modern Enna, where Euphemius died), retreating back to Mazara. In 830, they received a strong reinforcement of 30,000 African and Spanish troops. The Spanish Muslims defeated the Byzantine commander Theodotus in July and August of that year, but a plague once again forced them to return to Mazara and then to Africa. The African Berber units sent to besiege Palermo captured it in September 831 after a year-long siege. Palermo, renamed al-Madinah, became the Muslim capital of Sicily.
In February 832, Ziyadat Allah sent his cousin Abu Fihr Muhammad ibn Abd-Allah to the island and appointed him as the wāli of Sicily. He defeated the Byzantines in early 834, and in the following year his troops reached as far as Taormina. The war dragged on for several years with minor Ahglabid victories, while the Byzantines resisted in their strongholds of Castrogiovanni and Cefalù. New troops arrived in the island from the new Emir Al-Aghlab Abu Affan and occupied Platani, Caltabellotta, Corleone, Marineo, and Geraci, granting the Muslims total control of western Sicily.
In 836, Muslim ships helped their ally, Andrew II of Naples, when he was besieged by Beneventan troops, and with Neapolitan support Messina was also conquered in 842. In 845, Modica also fell, and the Byzantines suffered a crushing defeat near Butera, losing about 10,000 men. Lentini was conquered in 846, and Ragusa followed in 848.
In 851, the governor and general Al-Aghlab Abu Ibrahim died. He was succeeded by Abbas ibn Fadhl, the ferocious victor of Butera, Sicily. He started a campaign of ravages against the lands still in Byzantine hands, capturing Butera, Gagliano, Cefalù, and, most important of all, Castrogiovanni, in winter 859. Many of the captives from Castrogiovanni were sent to the Caliph Al-Mutawakkil, as a representation of Abbas ibn Fadhl's victory. In response, the Byzantine emperor sent a large army in 859–860 under Constantine Kontomytes, but the army and the fleet carrying it were defeated by Abbas. Byzantine reinforcements led many of the cities subjugated by the Muslims to revolt, and Abbas devoted the years 860–861 to reduce them. Abbas died in 861, replaced by his uncle Ahmed ibn Yaqub and, from February 862, by Abdallah, son of Abbas; the latter was in turn replaced by the Aghlabids with Khafagia ibn Sofian, who captured Noto, Scicli, and Troina.
In the summer of 868, the Byzantines were defeated for the first time near Syracuse. Hostilities resumed in the early summer of 877 by the new sultan, Jafar ibn Muhammad al-Tamini, who besieged Syracuse; the city fell on May 21, 878. The Byzantines now maintained control over a short stretch of coast around Taormina, while the Muslim fleet attacked Greece and Malta. The latter fleet was, however, destroyed in a naval battle in 880. For a while, it seemed that the Byzantines could regain Sicily, but new land victories for the Muslims re-established their control. A revolt in Palermo against Governor Seuàda ibn Muhammad was crushed in 887.
The death of the strong Emperor Basil I in 886 also encouraged the Muslims to attack Calabria, where the imperial army was defeated in the summer of 888. However, the first inner revolt was followed by another in 890, mostly spurred by the hostility between Arabs and Berbers. In 892 an emir was sent from Ifriqiya by Ibrahim II ibn Ahmad to Palermo but was ousted again a few months later. The prince did not relent and sent another powerful army to Sicily under his son, Abu l-Abbas Abdallah, in 900. The Sicilians were defeated at Trapani (August 22) and outside Palermo (September 8), the latter city resisting for another ten days. Abu l-Abbas moved against the remaining Byzantine strongholds and was also able to capture Reggio Calabria on the mainland on June 10, 901.
As Ibrahim was forced to abdicate in Tunis, he decided to lead in person the operations in southern Italy. Taormina, the last main Byzantine stronghold in Sicily, fell on August 1, 902. Messina and other cities opened their gates to avoid a similar massacre. Ibrahim's army also marched on southern Calabria, besieging Cosenza. Ibrahim died of dysentery on October 24. His grandson stopped the military campaign and returned to Sicily.
At this point, Sicily was almost entirely under the control of the Aghlabids with the exception of some minor strongholds in the rugged interior. The population had been somewhat increased by Muslim migrants from Iberia, North Africa, and the Middle East. The emir in Palermo nominated the governors of the main cities (qadi) and those of the less important ones (hakim), along with the other functionaries. Each city had a council called a gema, composed of the most eminent members of the local society, which was entrusted with the care of the public works and of the social order. The conquered Sicilian population lived as dhimmi or converted to Islam.
The Arabs initiated land reforms that increased productivity and encouraged the growth of smallholdings, a mere dent in the dominance of the landed estates. The Arabs further improved irrigation systems. With about 300,000 inhabitants, Palermo in the 10th century was the most populous city in Italy. A description of the city was given by Ibn Hawqal, a Baghdad merchant who visited Sicily in 950. A walled suburb called the Kasr (the citadel) was (and remains) the center of Palermo, and the great Friday mosque stood on the site of the later Roman cathedral. The suburb of Al-Khalisa (Kalsa) contained the sultan's palace, baths, a mosque, government offices, and a private prison. Ibn Hawqal reckoned there were 7,000 individual butchers trading in 150 shops.
In 909, the African Aghlabid dynasty was replaced by the Shiite Fatimids. Four years later, the Fatimid governor was ousted from Palermo when the island declared its independence under Emir Ahmed ibn-Kohrob. His first deed was a failed siege of Taormina, which had been rebuilt by the Christians; he was more successful in 914 when a Sicilian fleet under his son Mohammed destroyed the Fatimid fleet sent to recover the island. The following year, the destruction of another fleet sent against Calabria and the unrest caused by ibn-Kohrob's reforms led to a revolt of the Berbers.
The Berbers captured and hanged ibn-Kohrob, allegedly in the name of the Fatimid Caliph al-Mahdi, hoping he would leave them freedom of rule in Sicily. Al-Madhi instead sent an army which sacked Palermo in 917. The island was governed by a Fatimid emir for the following 20 years. In 937, the Berbers of Agrigento revolted again but after two resounding successes were decisively beaten at the gates of Palermo. An army was then sent by the new Caliph al-Qa'im to besiege Agrigento twice until it fell on November 20, 940. The revolt was totally suppressed in 941 with many of the prisoners sold as slaves and Governor Khalil boasting to have killed 600,000 people in his campaigns.
After suppressing another revolt in 948, the Fatimid Caliph Ismail al-Mansur named Hassan al-Kalbi as emir of the island. As his charge soon became hereditary, his emirate became de facto independent from the African government. In 950, Hassan waged war against the Byzantines in southern Italy, reaching up to Gerace and Cassano allo Ionio. A second Calabrian campaign in 952 resulted in the defeat of the Byzantine army; Gerace was again besieged, but in the end Emperor Constantine VII was forced to accept having the Calabrian cities pay a tribute to Sicily.
In 956, the Byzantines reconquered Reggio and invaded Sicily; a truce was signed in 960. Two years later a revolt in Taormina was bloodily suppressed, but the resistance of the Christians in Rometta led the new Emperor Nikephoros II Phokas to send an army of 40,000 Armenians, Thracians, and Slavs under his nephew Manuel, who captured Messina in October 964. On 25 October, the Byzantines were defeated in a fierce battle with the Kalbids. Manuel, along with 10,000 of his men, was killed in the fray.
The new Emir Abu al-Qasim (964–982) launched a series of attacks against Calabria in the 970s, while the fleet under his brother attacked the Adriatic coasts of Apulia, capturing some strongholds. As the Byzantines were busy against the Fatimids in Syria and with the partial conquest of the Bulgarian Empire, the German Emperor Otto II decided to intervene. The allied German-Lombard army was defeated in 982 at the Battle of Stilo. However, as al-Qasim himself had been killed, his son Jabir al-Kalbi prudently retreated to Sicily without exploiting the victory.
The emirate reached its cultural peak under the emirs Jafar (983–985) and Yusuf al-Kalbi (990–998), both patrons of the arts. The latter's son Ja'far was instead a cruel and violent lord who expelled the Berbers from the island after an unsuccessful revolt against him. In 1019, another uprising in Palermo was successful, and Ja'far was exiled to Africa and replaced by his brother al-Akhal (1019–1037).
With the support of the Fatimids, al-Akhal defeated two Byzantine expeditions in 1026 and 1031. His attempt to raise a heavy tax to pay his mercenaries caused a civil war. Al-Akhal asked the Byzantines for support while his brother abu-Hafs, leader of the rebels, received troops from the Zirid Emir of Ifriqiya, al-Muizz ibn Badis, which were commanded by his son Abdallah.
The local population conquered by the Muslims were Romanized Catholic Sicilians in Western Sicily and partially Greek speaking Christians, mainly in the eastern half of the island, but there were also a significant number of Jews.  These conquered people were afforded a limited freedom of religion under the Muslims as dhimmi, but were subject to some restrictions. The dhimmi were also required to pay the jizya, or poll tax, and the kharaj or land tax, but were exempt from the tax that Muslims had to pay (Zakaat). Under Arab rule there were different categories of Jizya payers, but their common denominator was the payment of the Jizya as a mark of subjection to Muslim rule in exchange for protection against foreign and internal aggression. The conquered population could avoid this subservient status simply by converting to Islam. Whether by honest religious conviction or societal compulsion large numbers of native Sicilians converted to Islam. However, even after 100 years of Islamic rule, numerous Greek speaking Christian communities prospered, especially in north-eastern Sicily, as dhimmi. This was largely a result of the Jizya system which allowed co-existence. This co-existence with the conquered population fell apart after the reconquest of Sicily, particularly following the death of King William II of Sicily in 1189.
In 1038, a Byzantine army under George Maniaces crossed the strait of Messina. This included a corps of Normans which saved the situation in the first clash against the Muslims from Messina. After another decisive victory in the summer of 1040, Maniaces halted his march to lay siege to Syracuse. Despite his conquest of the latter, Maniaces was removed from his position, and the subsequent Muslim counter-offensive reconquered all the cities captured by the Byzantines.
The Norman Robert Guiscard, son of Tancred, invaded Sicily in 1060. The island was split between three Arab emirs, and the Sicilian population rose up against the ruling Muslims. One year later, Messina fell, and in 1072, Palermo was taken by the Normans. The loss of the cities, each with a splendid harbor, dealt a severe blow to Muslim power on the island. Eventually all of Sicily was taken. In 1091, Noto in the southern tip of Sicily and the island of Malta, the last Arab stongholds, fell to the Christians. By the 11th century, Muslim power in the Mediterranean had begun to wane.
Many repressive measures were introduced by Frederick II to please the popes who were afraid of Islam close to the papal state.  This resulted in a rebellion by Sicilian Muslims, which in turn triggered organized resistance and systematic reprisals and marked the final chapter of Islam in Sicily. The Muslim problem characterized Hohenstaufen rule in Sicily under Henry VI and his son Frederick II. The annihilation of Islam in Sicily was completed by the late 1240s when the final deportations to Lucera took place.
The Adriatic port city of Bari, in the Apulia region of southern Italy, was captured by a Muslim army in 847, then remained under Muslim control for the next 25 years. It became the capital of a small independent Islamic state with an emir and a mosque of its own. The first ruler of Bari was Khalfun, a Berber leader who had probably come from Sicily. After his death in 852, he was succeeded by Mufarraq ibn Sallam, who strengthened the Muslim conquest and enlarged its boundaries. He also asked for official recognition from Baghdad Caliph al-Mutawakkil's governor in Egypt as wāli (i.e., prefect ruling over a province of the Abbasid empire). The third, and last, emir of Bari was Sawdan, who came to power around 857 after the murder of Mufarraq. He invaded the lands of the Lombard Duchy of Benevento, forcing duke Adelchis to pay a tribute. In 864, he obtained the official investiture asked by Mufarrag. The town was embellished with a mosque, palaces and public works.
Throughout the ninth century, Arab ships dominated the Tyrrhenian Sea. Their pirates prowled the Italian coast launching hit and run attacks against the cities of Amalfi, Gaeta, Naples, and Salerno. During this period, as the cities took command of their own defences, the Duchies of Gaeta and Amalfi gained their independence from the Duchy of Naples. The Christian states of the Campania were not yet prepared, however, to ally against the new Saracen threat. Amalfi and Gaeta regularly teamed up with the Saracens and Naples was hardly better, all much to the chagrin of the Papacy. In fact, it was Naples that first brought Saracen troops to the south Italian mainland when Duke Andrew II hired them as mercenaries during his war with Sicard, Prince of Benevento, in 836. Sicard immediately responded with his own Saracen mercenaries and the usage soon became a tradition. In 880 or 881, Pope John VIII, who encouraged a vigorous policy against the Muslim pirates and raiders, rescinded his grant of Traetto to Docibilis I of Gaeta and gave it instead to Pandenulf of Capua. As Patricia Skinner relates:
[Pandenolf] began to attack Gaeta's territory, and in retaliation against the pope Docibilis unleashed a group of Arabs from Agropoli near Salerno on the area around Fondi. The pope was "filled with shame" and restored Traetto to Docibilis. Their agreement seems to have sparked off a Saracen attack on Gaeta itself, in which many Gaetans were killed or captured. Eventually peace was restored and the Saracens made a permanent settlement on the mouth of the Garigliano river.
The Saracen camp at Minturno (in modern day Lazio) by the Garigliano River became a perennial thorn in the side for the Papacy and many expeditions were sought to get rid of them. In 915, Pope John X organised a vast alliance of southern powers, including Gaeta and Naples, the Lombard princes and the Byzantines; though, the Amalfitans stood aloof. The subsequent Battle of the Garigliano was successful, and the Saracens were ousted from any presence in Lazio or Campania permanently; though, raiding would be a continuous problem for another century.
In 898 the Abbey of Farfa was sacked by "Saracens", who burned it to the ground. Abbot Peter of Farfa managed to organise the community's escape and salvaged its library and archives. In 905, the monastery was again attacked and destroyed by "Saracens".
In 1480, an Ottoman Turkish fleet invaded Otranto, landing nearby the city and capturing it along with its fort. Pope Sixtus IV called for a crusade, and a massive force was built up by Ferdinand I of Naples, among them notably troops of Hungarian king Matthias Corvinus, despite frequent Italian quarreling at the time. The Neapolitan force met with the Turks in 1481, thoroughly annihilating them and recapturing Otranto.
Arabic art and science continued to be heavily influential in Sicily during the two centuries following the Christian reconquest. Frederick II, Holy Roman Emperor and King of Sicily in the early 13th century, is said to have been able to speak Arabic (as well as Latin, Sicilian, German, French, and Greek) and had several Muslim ministers. The heritage of the Arabic language can still be found in numerous terms adapted from it and still used in the Sicilian language. Another legacy of Muslim rule is the survival of some Sicilian placenames of Arabic origin, for example "Calata-" or "Calta-" from Arabic Qal`at… (قلعة), meaning "castle of".
Also, a genetic study in 2009 revealed a small but statistically significant genetic contribution of Northwest African genes among today's inhabitants near the city of Lucera.