Biotic homogenization caused by the invasion of non-native (alien) species is recognized as one of the main drivers of biodiversity erosion in island ecosystems. Conservation on islands is also often challenged by limited data on the distribution of remaining native habitats and threatened native and endemic species. We combine botanical survey data and habitat mapping through remote sensing and GIS to illustrate how multiple data sources can be used together to provide a synoptic view of the spatial distribution of native, naturalized and invasive alien plant species at an island scale, using the case study of Moorea (French Polynesia), a small (135 km²) tropical high volcanic island in the South Pacific. Results reveal that (i) 42 % of the rare and threatened native and endemic plant species are currently found in native habitats representing only 6 % of the island (8 km²); (ii) 49 % of these species occupy “hybrid” habitats covering 45 % of the island area (60 km²) where native species co-occur with naturalized non-native species; and (iii) 9 % of these species occur in 17 % of the island (23 km²) considered “novel” habitats that are highly invaded by alien plants that form dense monotypic stands. We conclude that conservation efforts and priorities should not neglect these novel and hybrid habitats on Moorea where many rare and threatened plants are found. Innovative strategies adapted to current conditions should be emphasized on small islands where conservation resources are often limited.