Aureococcus anophagefferens, a globally distributed picoplankton species, plays a critical role as a primary producer in marine ecosystems, and is responsible for brown tides in coastal waters, which significantly impact local environments and shellfisheries. Despite its pronounced adaptability across diverse marine habitats—from open oceans to estuaries—the genetic diversity underlying its niche differentiation remains poorly understood. This study investigated the intraspecific genetic diversity of A. anophagefferens in China’s coastal waters and the western Pacific, employing a novel mitochondrial marker (trnD-dam1) to resolve fine-scale population structure. Three distinct genotypes were identified, each exhibiting distinct environmental preferences: Type I dominated brown tide blooms in eutrophic, warm, low-salinity estuaries in the Bohai and Yellow Seas, correlating strongly with elevated dissolved organic nitrogen. In contrast, Types II (prevalent in U.S. strains) and III prevailed in high-salinity habitats, and associated with coastal zones influenced by transoceanic currents. Spatial-temporal analyses revealed genotype succession during bloom dynamics, with Type I constituting over 80 % of the population during peak bloom phases and coexisting with Type II during non-bloom periods. Samples from the Kuroshio Current exclusively harbored Types II and III, suggesting that oceanographic transport facilitates their dispersal. These findings indicate that A. anophagefferens populations have undergone adaptive divergence to exploit local environmental gradients, with genotype-specific preferences for temperature, salinity, and nutrient regimes shaping their biogeographic distribution.
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