There is increasing evidence for morphological change in response to recent environmental change, but how this relates to fluctuations in geographic range remains unclear. We measured museum specimens from two time periods (1902–1950 and 2000–2008) that vary significantly in climate to assess if and how two high elevation contracting species of ground squirrels in the Sierra Nevada of California, Belding's ground squirrel (Urocitellus beldingi) and the golden-mantled ground squirrel (Callospermophilus lateralis), and one lower elevation, stable species, the California ground squirrel (Otospermophilus beecheyi), have responded morphologically to changes over the last century. We measured skull length (condylobasal length), an ontogenetically more labile trait highly correlated with body size, and maxillary toothrow length, a more developmentally constrained trait predictive of skull shape. C. lateralis and U. beldingi, both obligate hibernators, have increased in body size, but have not changed in shape. In contrast, O. beecheyi, which only hibernates in parts of its range, has shown no significant change in either morphometric trait. The increase in body size in the higher elevation species, hypothesized to be a plastic effect due to a longer growing season and thus prolonged food availability, opposes the expected direction of selection for decreased body size under chronic warming. Our study supports that population contraction is related to physiological rather than nutritional constraints.