Environmental variation over a species's range creates differing pressures to which organisms must adjust in order to survive. Taxa can respond to these pressures at population and individual levels, leading to localized phenotypic differentiation. Assessing the spatial distribution of phenotypic variation can illuminate how dramatically varying environmental factors shape phenotypes and may forecast a taxon's ability to adapt should conditions change. We characterized morphological variation along a transect sampled in the Grinnell Resurvey project to determine whether Gambel's white-footed mouse (Peromyscus maniculatus gambelii), a generalist taxon inhabiting the full elevational range of habitats in Yosemite National Park and surrounding areas, has responded morphologically to variation in its environment. We quantified variation in modern P. m. gambelii cranial shape using 2D generalized Procrustes analysis and Euclidean distance matrix-based geometric morphometrics. We performed multivariate regression of shape coordinates on elevation to test for environmental influences on shape within the principal geographic dimension of change along the transect. We observe a statistically significant correlation with shape on elevation for occlusal and lateral views of the cranium, explaining a small percentage of the overall variation in shape. Modern P. m. gambelii crania show a pattern of flexion in which the angle of the cranial base decreases at higher elevations. Results of EDMA parallel these findings, but highlight additional areas of the cranium that vary with elevation. Collectively, the patterns of variation detected suggest a biological response to the environment that warrants further study. This work lays the foundation for comparison with morphological data from historical specimens, which can address evolutionary scenarios generated from our findings, and for investigation of other taxa included in the resurvey project. J. Morphol. 271:897–909, 2010. © 2010 Wiley-Liss, Inc.