Accurate species delimitation is a central assumption of biology that, in groups such as the Crocodylia, is often hindered by highly conserved morphology and frequent introgression. In Africa, crocodilian systematics has been hampered by complex regional biogeography and confounded taxonomic history. We used rigorous molecular and morphological species delimitation methods to test the hypothesis that the slender-snouted croco- dile (Mecistops cataphractus) is composed of multiple species corresponding to the Congolian and Guinean biogeographic zones. Speciation probability was assessed by using 11 mitochondrial and nuclear genes, and cranial mor- phology for over 100 specimens, representing the full geographical extent of the species distribution. Molecular Bayesian and phylogenetic species deli- mitation showed unanimous support for two Mecistops species isolated to the Upper Guinean and Congo (including Lower Guinean) biomes that were supported by 13 cranial characters capable of unambiguously diagnos- ing each species. Fossil-calibrated phylogenetic reconstruction estimated that the species split + 6.5 – 7.5 Ma, which is congruent with intraspecies diver- gence within the sympatric crocodile genus Osteolaemus and the formation of the Cameroon Volcanic Line. Our results underscore the necessity of com- prehensive phylogeographic analyses within currently recognized taxa to detect cryptic species within the Crocodylia. We recommend that the com- munity of crocodilian researchers reconsider the conceptualization of crocodilian species especially in the light of the conservation ramifications for this economically and ecologically important group.