There is still no uncontroversial agreement on the geographical variation, subspecies taxonomy and phylogenetic relationships between major populations of the lion Panthera leo. This study examines the patterns of geographical variation and phylogenetics of lions based on an extensive morphometric analysis on 255 wild lion skulls. The results of multivariate analysis of craniometric data indicate that lion skulls vary considerably throughout their geographical range and that the variation is greater within populations than between them, a significant subdivision being found only between sub-Sahara Africa and North Africa/Asia. Geographical variation is considerably affected by sexual dimorphism. Distance-based phylogenetic analysis [neighbour joining (NJ) and UPGMA], constructed from craniometric dissimilarities, not only confirmed the results of multivariate analyses but also fully corroborates current molecular genetic studies. The NJ and UPGMA trees show that the modern lion contains two major evolutionary clusters: the sub-Sahara Africa and North Africa/Asian lion, and also support the Late Pleistocene cave lion (Panthera leo spelaea) and modern lions as two distinct sub-clades, but they are more closely related to each other than to other Panthera. Further investigations focusing on the systematic position of the West African lion are urgently required.