The terrestrial flora and vegetation of Clipperton (La Passion) atoll, a very remote and small (170 ha of land) French island located in the North-Eastern Pacific Ocean, at ca. 1,000 km west of the Mexican coast, have dramatically changed during the past three centuries. This paper, based on historical testimonies, previously published floristic studies, and an extensive plant inventory conducted during the “International Scientific Expedition PASSION 2015,” show that the atoll has experienced particularly active and rapid vegetation dynamics with alternating plant cover expansion and regression phases. Our results provide the first comprehensive assessment of vegetation cover and vascular plant species distribution based on georeferenced data and mapped with GIS software, as well as the first record of two newly established non-native weeds. The current composition and abundance of native and alien vascular plant communities (15 species including only 4 native taxa) appear to depend not only on abiotic factors (e.g. substrate and climatic events) but also on biotic interactions with animal communities (e.g. native seabirds and crabs). Anthropogenic activities and disturbances (e.g. coconut palm, pig, rat and weed introductions) that have occurred in the past 100 years have also played an important role in explaining the past and current floristic changes.