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[Display omitted] • Nektonic communities exhibited strong spatial and temporal (Seasonal) patterns in coastal areas. • Phylogenetic clustering was found in spring nektonic communities of Dapeng Bay. • Mid-summer fishing moratorium increased stochasticity in structuring nektonic communities. • Fishing intensity is a strong stress for nektonic communities that even exceeds the effect of environmental impact. Coastal areas are important habitats for many species and strongly affected by anthropogenic activities. Management for sustainable coastal ecosystems benefits from a comprehensive assessment of species diversity. Here, we measured the spatio-temporal changes in community and phylogenetic structure of spring and autumn nektonic communities in Daya and Dapeng Bay among 12 sampling sites. We found that both the community structure and phylogenetic facets of nektonic communities in Daya and Dapeng Bay exhibited strong spatial and temporal patterns due which we attribute to fishing intensity and mid-summer fishing moratorium. The relatively larger ratio of unexplained variation in the autumn community resulted from stochastic processes caused by the mid-summer fishing moratorium. Furthermore, the phylogenetic structure of the spring nektonic communities between Dapeng and Daya Bay were significantly different; obvious phylogenetic clustering was found in spring nektonic communities of Dapeng Bay. These results implied that we may consider the current fishing intensity as a strong stress for nektonic communities, which exceeds the effect of natural processes and environmental factors. We speculate that the immediate sweeping fishing efforts may rapidly deplete the recovered fish stocks in a short time as human activities exert great stress on the nektonic communities in the study area. To avoid permanent damage to the ecosystem and a loss of valuable marine resources, urgent attention is required for fishery management. [ABSTRACT FROM AUTHOR]