Few studies have investigated the relationship between morphological variation and local feeding habits of bats in the United States. We used discriminant function analysis (DFA) to compare cranial morphology of Myotis occultus from southern Colorado, and central, and southern New Mexico. We analyzed guano collected from maternity colonies in southern Colorado and central New Mexico to compare food habits. Bats from southern Colorado had the smallest values on the first canonical variate (CV1) that also reflected the smallest measurements of key cranial and dental variables, including height of coronoid process, width of molar, and dentary thickness. Bats from central and southern New Mexico had intermediate and large CV1 values, respectively. Overall, CV1 discriminated individuals occurring in southern Colorado and central New Mexico from those in southern New Mexico. CV2 served best at discriminating bats of southern Colorado from those of central New Mexico. Comparison of food habits revealed that individuals from southern Colorado ate more soft-bodied prey items (e.g., flies) whereas bats from central New Mexico ate more hard-bodied prey items (e.g., beetles). As shown in earlier studies that investigated relationships between morphology and diet of insectivorous bats, we found differences in skull morphology of M. occultus that were correlated with differences in food habits.