Abstract: Urban wetland is an important part of the urban ecosystem that has multiple ecological and social service functions. Single-celled eukaryotic protists are main components of the material and energy flows in wetland ecosystems, and they are sensitive indicators for wetland ecological functions and health. We used 18 S rRNA gene（V9 region） amplicon sequencing method to profile protists communities of two typical urban wetlands in Heilongjiang province, a case study on marshy Longfeng wetland and Hulan estuary wetland of river type. A total of 5 713 operational taxonomic units（OTU） were obtained. Protists biodiversity and communities in two wetlands were investigated by analyzing taxonomic classification and relative abundance, α-diversity, β-diversity, principal coordinate analysis（PCoA）, and redundancy analysis（RDA） with environmental factors. The results showed that:（1）Protists from 24 phyla, 74 classes, 114 orders, 135 families, and 265 genera were identified;（2）The spatial distribution of the protists communities in two wetlands was significantly different;（3）Dissolved oxygen, water temperature and salinity were the most influential environmental factors for protists communities. This study used high-throughput sequencing method to investigate the protists of typical urban wetlands in Heilongjiang province, which will help to comprehensively and systematically understand protists communities of urban wetlands in alpine and high latitudes, and will provide the basis and reference for water environment monitoring and health assessment of Longfeng and Hulan estuary wetlands.