Abstract: Based on the fish monitoring data of shallow reefs along the Yongxing and Qilianyu Island from 2005 to 2013, we have adopted taxonomic diversity index, relative abundance and similarity index to study the species composition and the biodiversity of the coral reef fishes.The result indicates that the coral reef fishes belong to 4 orders 25 families 61 genera and 131 species, with an average family diversity index of 3.03, genera diversity index of 2.71 and normalization G-F index of 0.13.The number of species and relative abundance of Perciformes outweigh all other orders.The coral reef fishes along the Yongxing and Qilianyu Island were characteristics of more species diversity but low similarity.Due to coral reef degradation, strong fishing activities and the overfishing, the density of coral fishes showed a downward trend from 3.10/m² in 2005 to 1.23/m² in 2013.Reef fishes with small individual size, str-onger swimming capacities and the body length at 6.00 cm to 10.00 cm is more suitable for the area.