New World leaf-nosed bats (family Phyllostomidae) are one of the most diverse mammalian families and Artibeus is the most speciose phyllostomid genus. In spite of their species diversity, previous work on Artibeus crania using linear morphometrics has uncovered limited interspecific variation. This dearth of shape variation suggests a lack of niche partitioning across species, many of which are often found in sympatry. Using 2D geometric morphometric methods on a large sample of crania from eleven species from the Artibeus species complex (Artibeus and Dermanura), the current study demonstrates substantial cranial interspecific variation, sexual dimorphism, and intraspecific geographic variation. The majority of species were shown to have a unique size and shape, suggesting that each species is taking advantage of different niches. Both sexual size and shape dimorphism were significant in the Artibeus species complex. Artibeus species are known to have sex specific foraging strategies. The presence of cranial sexual dimorphism in the Artibeus species complex, combined with previous work showing that different fruit size and hardness is correlated with different cranial shapes in phyllostomids, indicates that the males and females may be utilizing different food resources, which has led to divergent cranial morphotypes. Finally, significant geographical shape variation was found in a large intraspecific sample of Artibeus lituratus crania. However, this variation was not correlated with latitude and instead may be linked to local environmental factors. Additional work on ecology and behavior in the Artibeus species complex underlying the morphological variation uncovered in this study will allow for a better understanding of how the group has reached its present diversity.