The effects of microhabitat differentiation on small-scale plant community structure in the Chiuhuahuan Desert were studied using multivariate analysis. The results showed that microhabitats (i.e., kangaroo rat mounds, ant mounds, shrubs, half-shrubs, and open areas) played a critical role in structuring small-scale plant community structure and maintaining species diversity. Annual plants were much more sensitvive to the presence of differentiated microhabitats than perennials and winter annuals exhibited stronger microhabitat perferences than summer annuals. Species diversity was highest on ant mounds while open areas supported the lowest diversity during both winter and summer. Biomass was highest in the shrub habitats followed by kangaroo rat mounds, ant mounds, half-shrubs, and open areas. Much of the diversity of these plants could be explained by the individualistic responses of species to the biotic effect of other plants or to disturbance by animals, or individualistic responses of species to differences in microenvironments.