The purpose of this study was to assess the influence of anthropogenic modification of coastal habitats on fish assemblages in Taiwan, comparing the abundance, species richness and taxonomic composition of fishes on natural v. artificial habitats. While there was no significant variation in the abundance or richness of fishes between natural and artificial habitats, the species composition of fishes in artificial habitats was significantly different from that of natural habitats. Natural reefs were characterized by greater abundance of Stethojulis spp. (Labridae), Abudefduf spp. (Pomacentridae) and Thalassoma spp. (Labridae), whereas anthropogenic habitats were dominated by Parupeneus indicus (Mullidae), Pempheris oualensis (Pempheridae) and Parapriacanthus ransonneti (Pempheridae). In general, it appears that specialist reef-associated species are being replaced with fishes that are much more generalist in their habitat-use. The loss of natural coastal habitats may threaten some species that cannot live in anthropogenically altered habitats, though the overall abundance and diversity of coastal fishes was not significantly different between natural and artificial habitats in Taiwan.