Habitat transformation caused by naturalized legumes has been considered as a profound environmental threat worldwide. However, the weight of the impact on species diversity of local native and naturalized flora has yet to be revealed. In order to gain a better understanding of the phenomenon, we developed and tested the following hypotheses: (1) naturalized legumes promote local species diversity; (2) naturalized legumes increase local naturalized species diversity rather than native biodiversity; and (3) the impact of naturalized legumes varies with habitat type. Four counties in Northern Taiwan were selected to form the study site. Nine major habitat types were identified in 100 sampling sites (1 km 2 /each site) in northern Taiwan, and a total of 2,242 plots (1 m 2 /each plot) were sampled. Species, cover, and biodiversity indices of both native and naturalized floras were obtained, and soil samples were collected from plots with and without naturalized legumes analyzed. The biodiversity and cover of the whole and naturalized flora were increased significantly by naturalized legumes, while no effects on native flora were found. The significant increase in the species diversity and cover of the whole flora and naturalized flora disappeared when naturalized legumes were excluded from the data set; the same trend was observed when habitat type was considered. Soil nitrogen was marginally significantly higher in the plots with naturalized legumes. The effects of naturalized legumes on native and naturalized floristic composition are divergent. Although species diversity and cover were increased by naturalized legumes, the additional species were naturalized legumes per se, which were the only beneficiaries of the enriched soil. The naturalized legumes did not facilitate further invasion by other exotic species, nor did they have an impact upon the native community in terms of cover, species diversity, or composition.