Understanding the spatial distribution of phenotypes and their association with local environmental conditions can provide important insights into the evolutionary history and ecological dynamics of species. Geographical variation in the skull size of the Artibeus lituratus complex was explored to evaluate the association between morphological traits and habitat-specific environmental conditions in the mainland populations of Middle and South America. We performed a principal component analysis based on 390 museum specimens using 17 cranial and mandibular measurements to explore the overall morphometric variation in our sample. Additionally, we used the information from 19 bioclimatic variables from 127 collecting localities to assess the extent of variation in environmental space across our study area. A canonical correlation analysis performed to evaluate the association between morphological and environmental variables indicated a high correlation between morphology and environment. Seasonality was correlated with skull size (canonical r = 0.7). Specifically, skull size in the A. lituratus complex increases as the amount of precipitation during the driest season increases and as inter-annual precipitation variability decreases. This result supports the hypothesis that environmental pressures are at least partially responsible for the skull size differences observed. Moreover, the nonrandom distribution of individuals with different skull sizes suggests that environmental filtering plays a role in determining the geographical distribution of morphological variants. © 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 105, 623–634.