The historical data of fish survey in Dongsha Islands, Xisha 514 species were recorded in Dongsha Islands, 620 in Xisha & Zhongsha Islands, and 548 in Nansha Islands, respectively, which were less than expected and also below the average number in other reef waters elsewhere which have similar habitats with South China Sea. Additionally, we calculated the fish taxonomic diversity indices: the average taxonomic distinctness indices △⁺ in Dongsha, Xisha & Zhongsha and Nansha Islands were 55.1, 60.2 and 56.6, respectively; variation in taxonomic distinctness index were 121, 164 and 150 in those islands, respectively. All △⁺ values were lower than that of the continental shelf waters of East China Sea, while all values were higher than it. Regarding the species' and family's taxon level, we calculated the similarity coefficients between reef waters of South China Sea and Calamine Islands, Milne Bay, southwest continental shelf waters of Nansha Islands and northern continental shelf waters of South China Sea. The results indicated that there is greater difference in similarity coefficients on species level between Xisha & Zhongsha Islands and the other reef waters, but less difference occurred on family level, and all similarity values on species and family level are higher in reef waters than those in continental shelf waters. Moreover, with Kruskal-Wallis detection, we studied the relative species richness of associated reef fish families in South China Sea reef areas, Calamine Islands and Milne Bay, but no significance difference were found. Hihgter species diversity and lower taxonomic diversity are the main characteristics of large scale distribution patterns of diversity of fish in coral reef waters, South China Sea.