In Egypt, two species of Bagrus fish have been described based on morphometric, meristic and cytotaxonomical characteristics. These species are Bagrus bajad and Bagrus docmac. The accurate identification of these fishes is complicated by the high variation in their characters, similarity among species and in some cases by the size of the fish. In this paper, we used polymerase chain reaction (PCR) and restriction fragment length polymorphisms (RFLPs) analysis of the mitochondrial cytochrome b gene {Cyt b) for molecular identification of Bagrus spp. in Egypt. The present study aimed at evaluating such advanced molecular biological approaches for identification of Bagrus spp. Genomic DNA was extracted from the two species of Bagrus. About 1120 bp Cyt b gene was amplified by PCR using specific primers. The technique of restriction fragment length polymorphisms was used to identify the specific Cyt b gene for each species. Accl, Apol and Eaei restriction endonucleases would differentiate Cyt b sequences of Bagrus bajad and Bagrus docmac into one group. .BseRl, BsrriBl, Dra, BsaOl, Xmdill, Aatl, BamHl and EcoRl restriction endonucleases differentiated the two species as a polyphylogenetic relationship