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Surface sediment samples were collected from sixteen sites of the southern Chinese coastline in this study. Diversity of eukaryotic microalgae was examined using high‐throughput sequencing of 18S rDNA to understand the community structure and geological distribution of microalgal resting stages. A total of 218 operational taxonomic units (OTUs) were detected for eukaryotic algae, and only 75 OTUs (34.40%) were detected into species level. The algal communities were composed of sixty‐four genera belonged to twelve classes of four phyla. Dinoflagellates were the most abundant and diversified group, which accounted for the average of 56.26% and 53.70% DNA reads and OTUs, respectively. Dinoflagellates were dominated by Protoperidinium , Euduboscquella , Amylax , and Paragymnodinium . Chaetoceros, Thalassiosira , and Skeletonema were abundant in diatoms, while Pedospumella and Paraphysomonas in Chrysophyceae were the most abundant genera due to their massive occurrence in some particular sites. The high abundance of Protoperidinium sequences suggested the high nutrient levels in the southern Chinese coastline. Nineteen of the detected OTUs were assigned to harmful and/or bloom‐forming microalgae. The wide occurrence of the toxic dinoflagellate Azadinium poporum and high abundance of Alexandrium pacificum in some particular sites suggested the potential risk of human poisoning.
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