Coastal and nearshore zones, severing as a connection between the land and the open ocean, are some of the most productive and complex ecosystems, where prokaryotes are abundant and highly diverse. However, the systematic study of the diversity of prokaryotes on a large-scale range in coastal and nearshore zones is limited due to scattered sampling sites, various sampling collection methods, and different data processing methods across various studies. Here, we provide a dataset of 16S rRNA gene sequences obtained from the surface water samples across the China Seas, including the Bohai Sea, the Yellow Sea, the East China Sea, and the South China Sea. The dataset comprises 1,194 samples collected through field sampling and literature search. A total of 30,308 operational taxonomic units clustered at 97% sequence identity were obtained. Sixty-five bacterial and nine archaeal phyla were identified. This dataset offers a basic understanding of prokaryotic diversity in the China Seas, also provides a foundation for in-depth investigations into prokaryotic distribution across different regions and their interactions in various environments.