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We examined the genetic diversity and connectivity of two indigenous Mediterranean goatfish species (Mullus barbatus and M. surmuletus), and a Lessepsian migrant species (Upeneus moluccensis), across the Nile Delta outflow using two mitochondrial DNA markers (COI and cyt b). Genetic diversity was high for the two Mediterranean species but relatively lower for the migrant species, suggesting founder effects after invasion from the Red Sea. Confirmation of this hypothesis, however, would require comparison with populations of origin in the Red Sea and the broader Indo-West Pacific. AMOVA and network analyses revealed no genetic partitioning for all species, indicating that the Nile outflow does not currently, and may not have historically, posed a significant barrier to larval dispersal in these goatfish, despite a present-day temperature and salinity gradient along the Mediterranean coastline of Egypt.