Habitat fragmentation and invasion by exotic species are regarded as major threats to the biodiversity of many ecosystems. We surveyed the plant communities of two types of remnant sagebrush-steppe fragments from nearby areas on the Snake River Plain of southeastern Idaho, USA. One type resulted from land use (conversion to dryland agriculture; hereafter AG Islands) and the other from geomorphic processes (Holocene volcanism; hereafter kipukas). We assessed two predictions for the variation in native plant species richness of these fragments, using structural equation models (SEM). First, we predicted that the species richness of native plants would follow the MacArthur–Wilson (M–W) hypothesis of island biogeography, as often is expected for the communities of habitat fragments. Second, we predicted a negative relationship between native and exotic plants, as would be expected if exotic plants are decreasing the diversity of native plants. Finally, we assessed whether exotic species were more strongly associated with the fragments embedded in the agricultural landscape, as would be expected if agriculture had facilitated the introduction and naturalization of non-native species, and whether the communities of the two types of fragments were distinct. Species richness of native plants was not strongly correlated with M–W characteristics for either the AG Islands or the **kipukas. The AG Islands had more species and higher cover of exotics than the kipukas, and exotic plants were good predictors of native plant species richness. Our results support the hypothesis that proximity to agriculture can increase the diversity and abundance of exotic plants in native habitat. In combination with other information, the results also suggest that agriculture and exotic species have caused loss of native diversity and reorganization of the sagebrush-steppe plant community.