Background <p>Species richness increases gradually as latitude decreases, however, the explanation for this phenomenon remains unclear. Ecological hypotheses suggest that greater niche diversity in tropical biomes may facilitate the coexistence of a larger number of species. The close relationship between species morphology and ecology can lead to a greater morphological disparity in tropical biomes.</p> Methods <p>In this study, we used 2D geometric morphometric techniques on the ventral view of the cranium of flying squirrels (Pteromyini, Sciuridae) to determine the relationship between diet and cranial morphology and to evaluate if morphological disparity is higher in tropical biomes.</p> Results <p>The results show that diet has a significant impact on cranial shape and size, with large, wide and robust crania in folivorous and generalist species, while frugivorous species tend towards smaller and narrower crania, and nucivorous have a wide variability. This suggests that biomes with more available dietary niches would show greater morphological disparity. However, we found no statistical differences in shape and size disparity among biomes or between observed and simulated disparity based on species richness.</p> Conclusions <p>Our results show that there are not disparity differences between tropical and temperate biomes, even when temperate biomes are less rich than tropical ones, suggesting that the quantity of available niches may not be the key factor in generating morphological disparity. Instead, it could be the presence of extreme niches that demand specialised adaptations for exploitation, which might be of greater significance. A greater importance of size-changing adaptations would decrease shape disparity in biomes with many niches.</p>