Recent interest in diagnoses and relationships between lineages of the alligator snapping turtle (Macrochelys temminckii) present conflicting patterns of molecular variation across the taxon's range. This study uses geometric morphometric techniques to test molecular hypotheses. We analyse alligator snapping turtle cranial variation amongst populations (i.e. drainages) with the hypothesis that populations of turtles recovered as monophyletic by previous molecular studies are more similar to each other in cranial shape. Dorsal, lateral and ventral cranial shape analyses corroborate the uniqueness of populations recovered by molecular genetic hypotheses. Additionally, analyses reveal near equal separation between drainages that were assigned to monophyletic clades by previous phylogenetic studies. These results reveal the potential for more independent lineages that have yet to be diagnosed, and unique cranial shapes are described for our three most heavily sampled drainages.