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Major regional gaps exist in the reporting and accessibility of naturalized plant species distribution data, especially within Southeast Asia. Here, we present the Malesian Naturalized Alien Flora database (MalNAF), the first standardized island-group level checklist of naturalized vascular plant species for the Malesian phytogeographical region. We used MalNAF to investigate the composition, origins, and habitat preferences of the naturalized flora. The naturalized vascular flora of Malesia consists of at least 1177 species. Richness is highest in the Philippines (539 spp.) and lowest in the Maluku Islands (87 spp.). But, the Lesser Sunda Islands had the highest naturalized species richness relative to native richness and Singapore has a higher naturalized plant species richness than would be expected given its size. When comparing the data for Malesia with a global dataset, we found that naturalized richness increased with area for islands but not for continental regions. Across the archipelago, 31 species are widespread, occurring in every island group, but the majority have a limited distribution of 2.4 ± 2.3 (mean ± SD) island groups per naturalized species. The naturalized plant species are representatives of 150 families, twenty of which are newly introduced to the region. Families richest in naturalized plant species in Malesia were Fabaceae (= Leguminosae) (160 spp.), Poaceae (= Gramineae) (138 spp.), and Asteraceae (= Compositae) (96 spp.). Most of these have a native range that includes tropical Asia, closely followed by those from Southern America (inclusive of the Caribbean, Central and South America), although at the island-group level, most have a higher proportion with a Southern American native range. Most naturalized species occur in anthropogenic habitats, but many are present in “natural” habitats with fewer species, such as Leucaena leucocephala, reported from specialized habitats like drylands. MalNAF provides a baseline for future studies of naturalized plant species distributions in the region.