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Changes in body size inversely related to ambient temperatures have been described in woodrats (Neotoma) over time scales ranging from decades to millennia. However, climate-mediated variation in other traits has not been evaluated, and the effects of precipitation have been overlooked. We assessed variation in skull morphology among bushy-tailed woodrats (Neotoma cinerea) over two sampling transects spanning coastal rainforest and interior desert environments to determine whether skull morphology varied with climate. We also tested whether previously described size-temperature relationships could be generalized to our study populations. In both transects, linear measurements of functionally significant traits differed between coastal and interior populations. Geometric morphometric analyses of shape confirmed some of those differences and revealed additional patterns of skull variation. Variation in some linear measurements, including body size, was predicted by climate. However, body and skull size, as well as measurements of skull components, displayed varying responses. Although longitudinal patterns of body size variation supported Bergmann’s rule, skull size variation was only weakly associated with climate. The strongest phenotypic responses to climate were those of auditory, dental, and palatal skull traits. Altogether, our findings suggest that geographic variation in temperature and precipitation mediated selective heterogeneity and plasticity in skull traits associated with food processing and sensory organs in N. cinerea. This was consistent with our expectation of resource-dependent phenotypic variation among populations in environments with highly contrasting climatic regimes.