Dinoflagellates are among the most significant phytoplankton groups in coastal waters, frequently forming blooms under favorable environmental conditions; however, the underlying biological and physical mechanisms remain poorly understood. From January 2025 to January 2026, we conducted a weekly survey in the eutrophic Xiamen Bay, integrating microscopy and DNA metabarcoding to investigate phytoplankton dynamics. During the study period, dissolved inorganic nitrogen (DIN) concentrations ranged from 22.8 to 109.8 μM, while dissolved reactive phosphorus (DRP) levels fluctuated from below detection limits to 1.7 μM. Although diatoms generally dominated the phytoplankton assemblage, with two distinct Skeletonema peaks in January and July 2025, a massive dinoflagellate bloom of Prorocentrum redfeldii (peaking at 1.5×10⁸ cells/L) occurred in January 2026. This bloom was localized within a stagnant area and coincided with a sudden rise in air temperature and a sharp decrease in wind speed. Furthermore, by characterizing ribosomal DNA sequences of P. redfeldii strains from the Yellow Sea and the East China Sea, we identified three distinct ribotypes with varying global biogeographical distributions. Both ribotypes A and B were present in the winter bloom, suggesting a preference for cold-water conditions—a finding supported by previous data showing ribotype B dominance during a 2018–2019 survey in Xiamen Bay. In contrast, ribotype C appears restricted to the Yellow Sea and other temperate regions. Our findings highlight the broad distribution of P. redfeldii and suggest potential ecological differentiation among its ribotypes.