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Abstract Plankton plays important roles in the marine ecosystems as important producers for primary production, major components in the global biogeochemical cycles, and the foundation of the marine food web. Despite their importance, long-term monitoring data about marine plankton are fairly limited, especially in the Asia-Pacific region. We fill this knowledge gap by providing a 29-year long-term monitoring data on the coastal areas of western Taiwan quarterly from 1993 to 2021. This long-term monitoring data can be used to set proper baseline for detecting human-induced impacts on the plankton, as well as modelling future scenarios under global changes.