The extensive diversity in dental form across mammals and its strong relationship with function provides insights into the diet, habitat, and behavior, of both extant and extinct taxa. Understanding the extent of variation in dental morphology across species allows for more accurate identification of fossils and a better ability to infer relationships between form and function and ecology. We examined variation in the size and shape of the first upper molar among the genus Neotoma. We employed elliptical Fourier analysis to quantify differences in the shape of 2D outlines for 23 populations and six species of Neotoma, varying in body size and habitat preference. As expected, molar length is a strong predictor of body size and is significantly and negatively correlated with temperature, particularly in species whose ranges span large latitudinal gradients. We found that differences in molar shape separate species into three general morpho-groups, with no evidence of a phylogenetic signal. While outline analysis could not robustly classify all molars to the species level, it did perform well for Neotoma cinerea, probably because of the greater degree of folding and more acute angling of molar lophs. In contrast, wider lophs with shallower enamel infolding was characteristic of species specializing on softer, more succulent resources (i.e., Neotoma albigula and Neotoma micropus). Neotoma floridana were inaccurately classified to species in the majority of cases, but were the only molars correctly identified to locality 100% of the time, suggesting that dietary specializations at a local level may drive morphological changes within the species as well as across the genus.