Environmental DNA Metabarcoding Reveals Distinct Spatial and Seasonal Patterns in Offshore Fish Communities in Eastern and Western Taiwan

ABSTRACT The spatiotemporal distribution of marine organisms in Taiwan is influenced by the convergence of three major water masses and the East Asian monsoon system. However, most studies on marine fish communities have focused on larval stages due to sampling limitations. To address this gap, we applied environmental DNA (eDNA) metabarcoding to assess fish diversity across three spatial scales and four seasons and to identify environmental drivers shaping these patterns. In 2023, a year‐long eDNA survey at 24 offshore sites detected 1026 marine fish taxa. The results revealed strong spatial and seasonal variation in community composition, closely tied to regional oceanography. In Eastern Taiwan, fish assemblages were mainly influenced by the Kuroshio Current, with distinct patterns in the northeast likely shaped by upwelling. In Western Taiwan, seasonal changes in northern communities reflected alternating dominance of water masses from the South China Sea and China coastal shelf, whereas southern communities remained relatively stable under the combined influence of the South China Sea Surface Current and a Kuroshio Branch. These findings advance our understanding of offshore fish biodiversity dynamics in Taiwan and highlight the role of oceanographic processes in shaping community structures, offering critical insights for long‐term monitoring and marine ecosystem management.