Objective  Xiamen Bay is located in the southeast of Fujian Province. It is rich in nutrients and has a strong biological basis. It is an important place for spawning, breeding, feeding and inhabiting of various fishery resources. In order to study the diversity and community structure of nekton in Xiamen Bay estuary.

Methods  Based on the data of bottom trawl survey of fishery resources in Xiamen Bay estuary in August 2023, the study used the methods of relative importance index, resource density index, biodiversity index and cluster to conduct research. The study analyzed the species composition, dominant species, resource density, species diversity and community structure characteristics of nekton.

Results  Results revealed a total of 147 nekton species captured during the survey period, spanning 107 genera within 63 families across 19 orders. Among these, there were 92 species of fish, 8 species of cephalopods, 8 species of stomatopods, 13 species of shrimps and 26 species of crabs. The average weight density and quantity density of nekton were 450.58 kg/km² and 4.42×10⁴ ind/km². Dominant species included Parapenaeopsis hardwickii, Parapenaeopsis cultrirostris, Oratosquilla oratoria, and Metapenaeopsis barbata.The Margalef richness index D ranged from 5.68 to 10.23, indicating moderate species richness. Shannon-Wiener diversity index H'_N and Pielou evenness index J'_N, based on individual number, varied between 1.47−3.34 and 0.38−0.88, respectively. Similarly, Shannon-Wiener diversity index H'_W and Pielou evenness index J'_W, based on biomass, ranged from 2.09 to 3.41 and 0.54 to 0.87, respectively. Hierarchical clustering and non-metric multi-dimensional scaling analysis delineated two distinct station groups within the estuary of Xiamen Bay: northern and southern. The results of NMDS sorting and CLUSTER hierarchical clustering analysis were relatively consistent. P. hardwickii and P. cultrirostris emerged as the primary dissimilar contributing species to these groups.

Conclusion The number of species in this survey is more than that in Xiamen Bay and Jiulong River estuary in recent years, and the dominant species were small, low trophic level and short life cycle species. These indices collectively indicated an overall moderate to high diversity level. The average species diversity index indicated an overall moderate diversity level. Catch miniaturisation is evident. Affected by the decline of fish resources, shrimp resources with short life cycle and strong fecundity have become an important supplement to fishery resources.

Significance This study supplements the basic data of nekton community in Xiamen Bay, and provides a scientific basis for the protection and management of ecosystem diversity in this sea area.