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The Nile crocodile Crocodylus niloticus currently has an extensive range throughout the African continent and Madagascar, though fossil and subfossil remains show that its historic range was considerably larger and included parts of the Sahara Desert, Mediterranean coast, and Arabian Peninsula. Recent molecular studies have yielded genetically distinct populations of C. niloticus, leading to the possibility that C. niloticus is actually multiple cryptic species, while morphological variation remains unassessed. This study compares skulls of C. niloticus to other members of the genus Crocodylus in dorsal view using geometric morphometrics to evaluate intraspecific and interspecific variation. The morphometric analysis is coupled with a geographic analysis to determine if the species is morphologically variable by geographic region as well as a model-based cluster analysis to determine and morphological clusters irrespective of other factors. These analyses indicate that C. niloticus exhibits populational variation that exceeds almost every other species of Crocodylus, with differences between geographic regions statistically disctinct. These results support the presence of a cryptic species complex. Additionally, an osteological description of Crocodylus niloticus is provided.