Despite a broad distribution, general habitat requirements, and a large dispersal potential, bobcats (Lynx rufus) exhibit a genetic division that longitudinally transects central North America. We investigated (1) whether the climate of the Last Glacial Maximum (LGM; 21 kya) isolated bobcats into refugia and also whether the current climate influences gene flow between the segregate populations and (2) whether the geographical patterns in cranial morphology reflect population identity. We created ecological niche models (ENMs) to evaluate climatic suitability and to estimate distributions of the disparate populations under both historical (LGM) and contemporary conditions. We used two-dimensional geometric morphometric methods to evaluate variations in the cranium and mandible. These variations were then regressed across geographical variables to assess morphological differences throughout the range of the bobcat. ENMs projected onto LGM climate provided evidence of refugia during the LGM via increased suitability in the north-west and south-east portions of this species' range. Contemporarily, our models suggest that the Great Plains may be restricting bobcat migration and gene flow, effectively maintaining disparate populations. Morphological analyses identified a significant linear trend in shape variation across latitudinal and longitudinal gradients rather than distinct morphological divergence between lineages. Similar shape variations, however, did converge in approximate locations of assumed refugia. The findings of the present study provide a robust assessment of the biogeographical considerations for the population genetic structure of bobcats.