Characterizing habitat associations of species is fundamental to understanding the mechanistic basis of community organization. Typically, investigators estimate microhabitat characteristics that account for significant amounts of variation in species composition. Nonetheless, highly resolved microhabitat characteristics may account for no more variation in species composition than coarse macrohabitat distinctions, particularly in heterogeneous environments. We describe micro- and macrohabitat associations of 13 species of nocturnal rodents distributed across 31 communities within the Mojave Desert. Rodent species composition, biomass of 81 perennial plant species, representation of 9 soil and rock classes, and the percent cover of annuals and grasses were quantified. Communities also were assigned to macrohabitats based on qualitative characteristics. Multivariate analysis of variance indicated highly significant community-wide differences among macrohabitats and species-specific analyses of variance substantiated differences for all but 1 species analyzed. Microhabitat characteristics accounted for approximately 55% of the variation in rodent species composition. Moreover, microhabitat characteristics accounted for 17% variation in rodent species composition over and beyond that shared with macrohabitat distinctions. Micro- and macrohabitat perspectives provide complimentary insights into species composition of rodent communities. Edaphic features in particular represented important environmental heterogeneity that likely acts both directly on rodent species composition and indirectly through influencing variation in plant species composition. Indeed, the Mojave Desert is represented by a spatial mosaic of species-rich and compositionally dynamic rodent communities that will provide many insights into the coexistence of species at regional spatial scales.