The aims of this study are were to assess the fish taxonomic diverstity and protect its fishes of coral reef waters in Xisha Islands,which located in South China Sea.Based on the historical data on the fish species composition in coral reef areas in Xisha Islands,the recorded fish species composition was updated,which made the average taxonomic distinctnessΔ⁺ and G-F index be used to assess the fish species taxonomic diversity in 16 reefs in Xisha,respectively.The results showed that a total of 661 fish species belonging to 305 genera,93 families,and 25 orders were recorded.Among them,more species were recorded in Yongxing Island(351),Huaguang Reef(173)and Dong Island(160).Δ⁺ in Xisha was about 60.2,however,Δ⁺ in Zhongjian Island,Jinqing Island,Yuzhuo Reef and so on was significantly lower than that in Xisha Islands,andΔ⁺ in Xisha Islands was also lower than that both in continental shelf and estuary area.This shows that the relationship among fish species in tropical coral reef areas was closer than those areas.Meanwhile Δ⁺ of marine fish species in China seas generally displayed a positive relationship with latitude on a large scale.However, G-F index was dependent on the number of species in the reef,and higher number of species would make higher G-F index,while fitting effect between R_G-F index and natural logarithm number of species was much better than that of G-F index in the paper.The reason why G-F index in Shi Island was negative was discussed preliminarily,which might mainly be caused by the lower species richness and the key Y=-XLnX for measuring species diversity was not a monotonic function.It was concluded that as species richness in Yongxing Island,Huaguang Reef,Dong Island and so on was higher,these habitats should be specially protected.