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Aim: Worldwide, floras are becoming homogenized at global scales, but regional patterns vary. Here, we present the first assessment for the Malesian phytogeographical region in terms of the timing of introductions, direction, magnitude and drivers of floristic change due to alien plant naturalizations. Location: Malesian phytogeographic region, including Southeast Asia and the Pacific. Taxon: Tracheophyta (vascular plants). Methods: We compiled data on first records of naturalized plants in Malesia to investigate temporal trends in the rate and origin of introductions. We then calculated β‐diversity (including turnover and nestedness) for the native, naturalized and Anthropocene (native + naturalized) floras for each pair of island groups (36 pairs), and a homogenization index for the native and Anthropocene floras, using presence/absence data for 31,580 plant species. Mantel tests were used to investigate the geographic, climatic and anthropogenic correlates of dissimilarity and homogenization. Results: Around 75% of all naturalized species documented to date were already reported for the first time within Malesia prior to 1950. This has led to homogenization between the historic (native) and contemporary (Anthropocene) floras for all island group pairs. Turnover was the most important process for driving compositional dissimilarity between island groups in Malesia in the native and Anthropocene floras, but homogenization resulted from decreases in nestedness and turnover. Differences in average taxonomic homogenization for island groups were associated with differences in their level of anthropogenic modification. Main Conclusions: This study improves current understanding of the direction and drivers of floristic homogenization in one of the world's most diverse tropical regions. Alien plant introductions carry a long historical legacy in Malesia, and naturalizations of these plants have led to overall taxonomic homogenization of the region's flora. Expected increases in the magnitude of human modification, without appropriate policy, will likely lead to further reductions in the floristic uniqueness of island groups. [ABSTRACT FROM AUTHOR]