Aim The final island ontogeny of the general dynamic model (GDM) (i.e., before island submergence) in tropical oceans corresponds to the coral atoll stage. Here, we examined whether the species richness of native vascular plants (indigenous and endemic species) on atolls is controlled by spatial and/or physical processes. We also predicted that atolls strongly affected by anthropogenic disturbance would have lower native species richness than predicted by spatial and physical processes. Location Marshall Islands, Kiribati Islands, Nauru, Niue, Johnston, Cook Islands, French Polynesia and Pitcairn Islands (Pacific Ocean). Taxon Native vascular plants. Methods We used stepwise regression to test the relative influence of five biogeographic variables on native species richness. Relationships were assessed for the full set of 111 Pacific coral atolls, as well as for atoll subsets ranging from 9 to 45 atolls. An index of human impact was then estimated, and residuals in the regression model predicting species richness from biogeographic variables were compared with the level of human impact. Results A regression model including atoll area, highest atoll elevation, the stepping stone distances from the nearest raised atoll and volcanic island explained native species richness on the 111 Pacific coral atolls. Regression models for different archipelagos and atoll subsets were also significant. Endemic species richness was significantly linked with highest atoll elevation and the stepping stone distances from the nearest raised atoll. Residuals in the biogeographic regression model were barely related to human impact across the 111 atolls but were significantly related to human impact in the Kiribati atolls. Main conclusions Native species richness on atolls is mainly controlled by physical and spatial characteristics. However, anthropogenic disturbances have altered the predicted pattern of native species richness leading to a lower model fit in some atoll subsets.