Zones of secondary contact between closely related species provide a rare opportunity to examine evidence of evolutionary processes that reinforce species boundaries and/or promote diversification. Here, we report on genetic and morphological variation in two sister species of woodrats, Neotoma fuscipes and N. macrotis, across a 30-km transition zone in the Sierra Nevada of California. We assessed whether these lineages readily hybridize, and whether their morphology suggests ecological interactions favoring phenotypic diversification. We combined measurements of body size and 11 craniodental traits from nine populations with genetic data to examine patterns of variation within and between species. We used phylogenetic autocorrelation methods to estimate the degree to which phenotypic variation in our dataset arose from independent evolution within populations versus phylogenetic history. Although no current sympatry or hybridization was evident, craniodental morphology diverged in both lineages near their distributional limits, whereas body size converged. The shift in craniodental morphology arose independently within populations whereas body size retained a strong phylogenetic signal, yet both patterns are consistent with expectations of phenotypic change based on different models of resource competition. Our findings demonstrate the importance of examining a suite of morphological traits across contact zones to provide a more complete picture of potential ecological interactions: competition may drive both diversification and convergence in different phenotypic traits.