Abstract: On the basis of diatom analysis for 78 samples from 18 stations in surface sediments collected from coastal waters in southeast China and according to the distribution pattern of dominant and sub-dominant species,three assemblages and two subassemblages of diatoms were divided,corresponding to the three coastal waters of South China Sea,Taiwan Strait and East China Sea respectively. Statistics show that the distribution of diatoms in surface sediments in coastal waters has little relation with continental runoff.As water depth increases,the marine primary productivity decreases.Benthic species and intertidal species decreases while planktonic species increases.The distribution of assemblage Ⅰ shows that the northeastern South China Sea was significantly affected by the Kuroshio Current.The dominant and diagnostic diatom species in assemblages Ⅱ1 and Ⅱ2 can be used to indicate water depth, and their difference is a response to the currents from the two sides of the Taiwan Strait which are different in winter and summer times.The assemblage Ⅲ was obviously controlled by the coastal current with little effect from the Kuroshio current.