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Simple Summary: Coral reef fish diversity forms the foundation of their adaptability. A comprehensive understanding of coral reef fish diversity is crucial for the conservation of both coral reefs and their associated fish species. In this study, we employed three taxonomic diversity indices to analyze the characteristics and changes in taxonomic diversity within a representative coral reef (Meiji Reef) located in the South China Sea from 1998 to 2018. Fish species richness played a significant role in shaping the diversity of coral reef fish families and genera within the South China Sea region. Contrary to findings from 1998–1999, there had been a relative increase in fish family diversity at Meiji Reef during 2017–2018. Distribution patterns among different coral reef fish communities across taxonomic levels exhibited varying degrees of unevenness within the South China Sea region. The changes observed in the taxonomic distinctness index between 1998–1999 and 2016–2018 indicated greater dissimilarity among species relationships and reduced taxonomic uniformity. Coral reef fish are important groups of coral reefs, which have great economic and ecological value. Meiji Reef is a representative tropical semi-enclosed atoll in the South China Sea, with rich fish resources. Based on the data from hand-fishing, line-fishing, and gillnet surveys of fish in Meiji Reef from 1998 to 2018, this study summarized the fish species list of Meiji Reef and analyzed the species composition, inclusion index at the taxonomic level (TINCL), genus–family diversity index (G–F index), average taxonomic distinctness index (Δ+), and variation in taxonomic distinctness (Λ+) and their changes. The results revealed that from 1998 to 2018, there were 166 reef-dwelling fish species on Meiji Reef, belonging to 69 genera, 33 families, and 11 orders, of which 128 species were from 20 families of Perciformes, accounting for 77.10% of the total cataloged species. Regarding the dependence of fish on coral reefs, there were 155 reef-dependent species or resident species (accounting for 93.37%) and 11 reef-independent species or wandering species (accounting for 6.63%). The TINCL of the order, families, and genus of fish in Meiji Reef were very high. The genus diversity index (G index), family diversity index (F index), and G–F index of fish in Meiji Reef were very high, and the G index of fish in Meiji Reef in 1998–1999 was higher than that in 2016–2018. The Δ+ and Λ+ values of fish in Meiji Reef from 1998 to 2018 were 56.1 and 148.5, respectively. Compared with 1998–1999, Δ+ and Λ+ of fish increased during 2016–2018, reflecting that the relatives of fish in Meiji Reef became further distant, and the uniformity of taxonomic relationships among species decreased. The research findings indicated that fish exhibited a high taxonomic diversity in Meiji Reef; however, it also revealed significant fluctuations in the fish diversity of Meiji Reef over an extended period, emphasizing the urgent need for timely protection measures. This investigation significantly contributes to our comprehension of the intricate dynamics governing fish species within Meiji Reef and holds broader implications for biodiversity conservation in tropical marine ecosystems. [ABSTRACT FROM AUTHOR]

Highlights: What are the main findings? The commercial small pelagic fishes (Decapterus maruadsi and Trachurus japonicus) in the Beibu Gulf were still miniaturizing. Fisheries management, characterized by reduced fishing efforts, cannot completely restore population structure in a short period. What are the suggestions for the future fisheries development in the Beibu Gulf? Continuing to maintain low fishing mortality and increasing the catchable length should be the key ways to achieve fishery resource conservation and recovery. Simple Summary: Decapterus maruadsi and Trachurus japonicus, as the main commercial small pelagic fish in the coastal fisheries of China, have been facing the threat of population decline due to overfishing. In this work, we assessed the population status of two commercial small pelagic fish stocks in the Beibu Gulf (in the South China Sea) over the past 15 years (2006–2020). The analysis results show that the commercial small pelagic fishes in the Beibu Gulf were still miniaturizing, and fisheries management characterized by reduced fishing efforts cannot completely restore population structure in a short period. Continuing to maintain low fishing mortality and increasing the catchable length should be the key ways to achieve fishery resource conservation and recovery. Our findings will provide a key scientific basis for future improvements in offshore fisheries management. Long-term variations in population structure, growth, mortality, exploitation rate, and recruitment pattern of two major commercial small pelagic fishes (CSPFs) (Decapterus maruadsi and Trachurus japonicus) are reported based on bottom trawl survey data collected during 2006–2020 in the Beibu Gulf, South China Sea. All individuals collected during each sampling quarter over a period of 15 years were subjected to laboratory-based analysis. In this study, the stock of D. maruadsi and T. japonicus inhabiting the Beibu Gulf was assessed using length-based methods (bootstrapped electronic length frequency analysis (ELEFAN)) to complete stock assessment in different fishery management periods (the division of fisheries management periods was based on China's input and output in the South China Sea offshore fisheries over 15 years, specifically divided into period I (2006–2010), period II (2011–2015), and period III (2016–2020)). The results showed that the mean body length, dominant body size, and estimated asymptotic length of two CSPFs decreased, whereas their growth coefficient decreased, indicating miniaturization and slower growth, respectively. Estimated exploitation rates and catching body length for two CSPFs indicated that both stocks in the Beibu Gulf were overexploited in period I and moderately exploited after 2011. These stocks were taking a good turn in status in period III, with the exploitation rate much lower than the initial period and reversing the downward trend in catching body length. Furthermore, the variations in the spawning season of the two CSPF stocks and their barely satisfactory expected yield indicated the complexity of the current fishery management in the Beibu Gulf. These results suggest that management measures to reduce fishing pressure may have a positive influence on the biological characteristics of those CSPFs in the Beibu Gulf; however, the stock structure already affected by overfishing will be a huge challenge for the conservation and restoration of fisheries resources in the future. Given that the current stocks of D. maruadsi and T. japonicus in the Beibu Gulf still have low first-capture body length (Lc) and high fishing mortality (F) (compared to F0.1), we identify a need to refine population structure by controlling fishing efforts and increasing catchable size, and more consideration should be given to the local fishery resource status in fisheries management. [ABSTRACT FROM AUTHOR]