Aim: Rare species make substantial contributions to coastal ecosystem functions. Functional rarity (FR) and phylogenetic rarity (PR) are important features for biodiversity conservation. This work aimed to discuss the necessity and reasonableness of conserving fish FR and PR in coastal seas.Location: China.Methods: By compiling historical fish investigation data, joint species distribution modelling (JSDM) was applied to model fish communities in coastal China Seas. Biogeographic patterns of FR and PR were explored, and the effectiveness of current MPA networks in terms of match/mismatch with the hotspots of rarity was assessed.Results: A total of 44 functionally rare species and 22 phylogenetically rare species were identified. Six of these species were both functionally and phylogenetically rare, and only one was listed as endangered on the Red List of the International Union for Conservation of Nature (IUCN). Functional rarity hotspots covered 10.27% of the coastal areas, which geographically converged in the southern and eastern coast of Taiwan, the Yangtze River Estuary and the Yellow River Estuary. Phylogenetic rarity hotspots only covered 3.06% of the coastal areas, which were sporadically distributed in the coastal East China Sea, the Bohai Sea and the northern Yellow Sea. Current marine‐protected areas (MPAs) only represented 16.16% of the FR hotspots and 20.48% of the PR hotspots, indicating substantial mismatched areas between the MPAs and the hotspots of FR and PR.Main Conclusions: Only considering threatened species in conservation practices will omit functionally and phylogenetically rare species because FR and PR are not necessarily correlated with species threat status on the IUCN Red List. Functional rarity hotspots do not necessarily overlap with PR hotspots, and current MPAs mismatch the majority of these areas. We therefore advocate that conservation prioritization and expansion of MPA networks should account for FR and PR both at the species and site levels.

Globally, marine fisheries have declined under multiple stresses including overfishing, climate change, and habitat degradation. The Min River Estuary, as the largest estuary in southeastern China, has confronted this situation over recent decades. In this study, the dominant species of fish stocks in the Min River Estuary, including Coilia mystus, Cynoglossus abbreviates, Collichthys lucidus, Amblychaeturichthys hexanema, Polydactylus sextarius, Harpodon nehereus, and Secutor ruconius, were evaluated by the length-based Bayesian biomass estimator method (LBB). Outcomes could be grouped into three categories as healthy, showing the lowest exploitation rate (E: 0.31–0.43) and highest relative biomass (B/B_msy: 1.30–1.90), including S. ruconius, C. mystus, and H. nehereus; overfished, with a medium E (0.50–0.58) and B/B_msy (0.68–0.79), including A. hexanema and C. abbreviates; and collapsed, with the highest E (0.89–0.92) and lowest B/B_msy (0.03–0.21), including C. lucidus and P.sextarius. Corresponding imperative countermeasures such as using larger-sized mesh gears and reducing fishing intensity should be deployed according to the current status of each species for sustainable fishery exploitation and fish conservation.

Poyang Lake, the largest freshwater lake in China, possesses abundant fishery resources, but its fish stock status is still unclear. In this work, the stock status of and fishing efforts of nine major economic fishes in the Poyang Lake were estimated from 2000 to 2019 with a catch-based maximum sustainable yield (CMSY) model based on catch and resilience data. It was further predicted whether the biomass of those fishes could be restored to support maximum sustainable yield (B_msy) under the policy of “Ten years fishing moratorium in the Yangtze River”. The results showed that goldfish Carassius auratus, grass carp Ctenopharyngodon idella, and black carp Mylopharyngodon piceus suffered from higher fishing efforts and low biomass in the past 20 years; bighead carp Hypophthalmichthys nobilis, yellow catfish Tachysurus fulvidraco, and common carp Cyprinus carpio responded differently to their fishing efforts; silver carp Hypophthalmichthys molitrix, Amur catfish Silurus asotus, and mandarin fish Siniperca chuatsi were underexploited. Six species were overfished in 2019, and their biomass would be expected to recover for sustainable exploitation during the fishing moratorium, except for M. piceus. This study provided a case study of feasible freshwater fishery evaluation in limnetic ecosystems.

To address uncertainties in how threatened coastal China seas fish communities respond to stressors like overfishing and climate change, this study applied Hierarchical Modelling of Species Communities (HMSC) to disentangle the assembly rules shaping these communities, filling a critical gap in understanding their spatiotemporal dynamics. We analyzed data on 384 fish species (1980–2018) and key environmental factors, with variance partitioning revealing that environmental filtering dominated fish distributions (explaining over 99% of variance), far outweighing random effects (0.60%). Among environmental drivers, sea surface temperature (49.00%) and sea surface salinity (33.25%) were the most influential, while seafloor substrate and water depth played secondary roles; notably, fewer species occupied fine sand habitats, and more preferred silt habitats. Residual species associations—indicative of potential biotic interactions—were most frequent within Gobiidae, likely due to this highly diverse taxon’s specialized resource utilization and wide distribution, highlighting that biotic filtering is concentrated and ecologically relevant within this group. This work demonstrates HMSC’s utility in unraveling coastal fish community assembly, providing a robust basis for predicting community changes and guiding biodiversity conservation efforts that support ocean health and dependent human activities.