| Summary: | Marine <i>Synechococcus</i> are an ecologically important picocyanobacterial group widely distributed in various oceanic environments. Little is known about the dynamics and distribution of <i>Synechococcus</i> abundance and genotypes during seasonal hypoxia in coastal zones. In this study, an investigation was conducted in a coastal marine ranch along two transects in Muping, Yantai, where hypoxic events (defined here as the dissolved oxygen concentration <3 mg L<sup>−1</sup>) occurred in the summer of 2015. The hypoxia occurred in the bottom waters from late July and persisted until late August. It was confined at nearshore stations of the two transects, one running across a coastal ranch and the other one outside. During this survey, cell abundance of <i>Synechococcus</i> was determined with flow cytometry, showing great variations ranging from 1 × 10<sup>4</sup> to 3.0 × 10<sup>5</sup> cells mL<sup>−1</sup>, and a bloom of <i>Synechococcus</i> occurred when stratification disappeared and hypoxia faded out outside the ranch. Regression analysis indicated that dissolved oxygen, pH, and inorganic nutrients were the most important abiotic factors in explaining the variation in <i>Synechococcus</i> cell abundance. Diverse genotypes (mostly belonged to the sub-clusters 5.1 and 5.2) were detected using clone library sequencing and terminal restriction fragment length polymorphism analysis of the 16S–23S rRNA internal transcribed spacer region. The richness of genotypes was significantly related to salinity, temperature, silicate, and pH, but not dissolved oxygen. Two environmental factors, temperature and salinity, collectively explained 17% of the variation in <i>Synechococcus</i> genotype assemblage. With the changes in population composition in diverse genotypes, the <i>Synechococcus</i> assemblages survived in the coastal hypoxia event and thrived when hypoxia faded out.
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