I compared vegetation and substrate characteristics at capture locations of three syntopic species of pocket mice (Chaetodipus: Heteromyidae) to determine differences in microhabitat affinities of these ecologically similar rodents in coastal Baja California, Me´xico. Principal components analysis revealed that capture locations of C. spinatus had disproportionately higher cover of medium and large rocks, and tended to have higher plant species diversity than capture locations of the other two species. C. spinatus and C. arenarius, the two smallest species, differed most in their microhabitat affinities, suggesting spatial segregation that may minimize competition for similar food resources. C. arenarius was captured most often at sites with the finest-textured soils, whereas C. rudinoris, the largest species, was widespread and frequently associated with gravel and small rocks. No species showed any apparent preference for plant species or significant amounts of overhead cover, a conclusion supported by the high densities of C. rudinoris on small, barren islands in the Gulf nearby. My results represent the first quantitative descriptions of the habitat associations of these species, which are wholly or predominantly restricted in their distributions to Baja California.