Human-mediated introductions of exotic species and extirpations of native species have modified the composition of biotic communities throughout the world, but the consequences of introductions and extirpations on local phylogenetic diversity (alpha-diversity) and on phylogenetic distinctiveness between sites (beta-diversity) remains poorly investigated. Here we analyze the long-term impacts of extirpations and invasions on both phylogenetic and taxonomic alpha and beta diversity of fish assemblages in Chinese isolated lakes. Data of fish assemblages in 15 lakes were grouped into three periods spanning the last 75 years: historical, intermediate and current periods. We partitioned phylogenetic beta diversity into turnover and nestedness component, and examined how introductions and extirpations led to temporal changes in alpha and beta diversity using linear regression and multiple regression models on distance matrices, respectively. Introductions and extirpations caused an increase of phylogenetic diversity (Delta(+)) and phylogenetic unevenness (Lambda(+)) within the lakes, but the phylogenetic dissimilarity between lakes declined. Such trend, resulting from 60 years introductions and extirpations, was mainly due to a decline of the phylogenetic turnover, indicating that the replacement of native endemic species by widespread exotic species was the main driver of the observed phylogenetic homogenization. Temporal changes in phylogenetic and taxonomic dissimilarities were positively correlated, and taxonomic homogenization causes phylogenetic homogenization in ca. 60% of the lake pairs. Nevertheless, taxonomic homogenization turns to phylogenetic differentiation in one third of lake pairs due to the extirpation of the closely-related species and the introduction of distinct exotic species belonging to different lineages among lakes. Therefore, measuring phylogenetic diversity changes provides complementary information to taxonomy, and gives support to the Darwin's naturalization hypothesis stipulating that species distantly related to natives easily establish in their introduction range. Our results demonstrate that half a century of anthropogenic disturbance was sufficient to blur the phylogenetic distinctiveness among lakes that resulted from the last 5 million years evolutionary history of the Yun-Gui plateau.