Abstract Aim Species richness of native, endemic, and exotic plant groups is examined relative to island area, disturbance history, geological history, and other physical characteristics. Of particular interest are the biogeographic factors that underlie (a) differences in species-area and species-isolation relationships between plant groups; and (b) adherence or departure of individual islands and/or plant groups from expected patterns. Location The eight Channel Islands lie along the continental margin between the U.S./Mexico border and Point Conception, CA. They range in size from 2.6 to 249 km2, and are located from 20 to 100 km off the coast. The islands are known for their high degree of plant endemism, and they have undergone a long history of human occupation by indigenous peoples, followed by over a century of intensive grazing and other biotic disturbances. Methods The study is based on linear regression and residual analysis. Cases where individual islands and/or specific plant groups do not adhere to patterns expected under species-area and species-isolation paradigms, are evaluated with respect to other island characteristics that are not captured by considering only island size and isolation. Results All three plant groups exhibit strong, positive relationships between species richness and island size. For native species, the variance that remains after consideration of island size is largely explained by island isolation. For exotic species, residuals from the species-area relationship are unrelated to isolation. For endemic species, residuals from the species-area relationship are negatively related to isolation. Several islands are outliers for endemic and exotic species, for which richness values are not explained by either island area or isolation. Main conclusions Species-area and species-isolation relationships for native, endemic, and exotic plant groups differ in accordance with hypothesized differences in the biogeographic factors that govern species diversity for these three groups. Most notably, endemic richness increases with isolation, suggesting the influence of this variable on processes of speciation and relictualism. These general relationships persist despite a long and varied history of human activity on the islands. Analysis of residuals suggests that deviations from expected patterns correspond to island-specific biogeographic factors. It is hypothesized that primary among these factors are land-use history, island environmental characteristics, and community-type richness.