Abstract: Fish taxonomic diversity is the basis of fish diversity protection and community stability analysis. Based on the monitoring and historical data of fishery resources in seven coastal waters of the northern South China Sea (Leizhou Bay, Daya Bay, Pearl River Estuary, Lingshui Bay, Hailing Bay, Fangchenggang and Nan'ao Island) during 2014 to 2017, we analyzed the species composition and spatial pattern of fish taxonomic diversity by studying the taxonomic diversity index and taxonomic dissimilarity index, in addtion with a cluster analysis. The results show that: 1) A total of 1 105 fish species had been identified. The species richness was the greatest in the Pearl River Estuary (958 species) and the least in Nan'ao Island (94 species). 2) The seven waters can be divided into two groups: Group I (Leizhou Bay, Pearl River Estuary and Daya Bay) had high taxonomic diversity and uneven genetic relationship; Group II (Lingshui Bay, Nan'ao Island, Hailing Bay and Fangchenggang) had low taxonomic diversity. 3) The variation range of average taxonomic distinctness index (∆⁺) in each water was small (54.3–61.04), and the variation of Δ⁺ was not positive with the increase of latitude. 4) The ∆⁺ of Lingshui Bay, Hailing Bay and Fangchenggang fell in the outside of the 95% confidence funnel. In conclusion, the tropical-subtropical characteristics of fish species in the surveyed area are generally obvious, with a decreasing trend of ∆⁺ of Bohai Sea>Yellow Sea>East China Sea>South China Sea; Lingshui Bay, Hailing Bay and Fangchenggang might have habitat degradation, which indicates that the research on fishery monitoring is necessary for the fishes biodiversity protection.