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There may have been two separate men named Alphaeus. Though both Matthew and James are described as being the "son of Alphaeus" there is no Biblical account of the two being called brothers, even in the same context where John and James or Peter and Andrew are described as being brothers.
Alphaeus is traditionally identified with Clopas, based on the identification from parallel Gospel accounts of Mary, the mother of James the third woman with Mary Magdalene and Salome wife of Zebedee beside the cross in Matthew with Mary, the wife of Clopas, the third woman in John's account.
The Catholic Encyclopedia suggest that etymologically, the names Clopas and Alphaeus are different, but that they could still be the same person. Other sources propose that Alphaeus, Clophas and Cleophas are variant attempts to render the Aramaic H in Aramaic Hilfai into Greek as aspirated, or K.