A dataset of distribution of toxic and harmful microalgae and algal toxins in China's coastal waters during 2019–2021

China's coastal waters, including the Bohai Sea, the Yellow Sea, the East China Sea and the South China Sea, are rich in marine resources and of strategic importance to the country's economic development. In recent years, the problem of water safety caused by algae and algal toxins is becoming more and more serious, and the frequency and scale of harmful algal blooms are increasing in China's coastal waters. This dataset collected and organized the survey data of toxic and harmful microalgae and algal toxins in China's coastal waters from 2019 to 2021, it included 3429 microalgae data, 33 240 microalgae molecular species data, 489 phytoplankton algal toxin data, 76 seawater algal toxin data and 440 economic species algal toxin data. The research teams providing the data ensured the accuracy of the test data through inter-project and international collation. In order to display the distribution of toxic and harmful microalgae and algal toxins in China's coastal waters, 115 microalgae distribution maps and 29 algal toxin distribution maps were provided. This dataset can provide data support for the study of the spatial and temporal distribution of toxic and harmful microalgae and algal toxins in China's coastal waters, and for the prevention, warning and control of harmful algal blooms.