A new species of Pseudoniphargus, P. longiflagellum (Crustacea Amphipoda) is described from subterranean freshwater of the Rifian region of Morocco. This species is closely related to the group P. ruffoi-P. longipes, which shares several apomorphic characters. The two step model of colonization and evolution provides an understanding of the origin and the age of this stygobite. P. longiflagellum is derived from marine ancestors which lived in the coastal groundwater of the Tethyan South-Rifian channel during the Miocene Tortonian period. The regression of this corridor during the late Tortonian period or at the beginning of the Messinian period may have played a major role in the evolutionary history through vicariance.