The northwestern Pacific (NWP) encompasses diverse oceanographic regimes, with the confluence of the warm Kuroshio and the cold Oyashio forming a seasonally shifting ecotone characterized by strong environmental contrasts that offers a unique natural laboratory to study marine biodiversity. However, the seasonal variation pattern and its drivers in the diversity of fish communities across the basin currently remain poorly understood. This study utilized environmental DNA (eDNA) metabarcoding to investigate seasonal variations in the diversity of fish communities at taxonomic, functional, and phylogenetic levels to assess the ecological processes shaping community assembly. Our findings reveal significant seasonal differences, with higher α diversity in summer, characterized by increased species richness, functional richness, and phylogenetic diversity, indicating increased primary productivity and favorable environmental conditions. β diversity results reveal that species turnover, rather than nestedness, plays the leading role in determining community structure, with greater turnover in summer influenced by dynamic oceanographic processes. Environmental factors, including net primary productivity and dissolved oxygen, show strong correlations with summer fish diversity, whereas geographic factors show a stronger association in autumn. Network analysis reveals stronger species interactions and greater ecological stability in summer, whereas lower connectivity and reduced network stability in autumn indicate increased susceptibility to disturbances. Additionally, stochastic processes, especially drift and dispersal limitation, were found to dominate fish community assembly across both seasons. These findings underscore the ecological importance of seasonal dynamics in the NWP, highlight mechanisms shaping fish biodiversity, and provide insights for season-specific conservation and sustainable fisheries management.
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