The distribution of diatoms in surface sediments in the Minjiang Estuary, southeast China, was investigated in 2009. Total 56 species and other species belonging to 25 genera were identified, among them 11 species were dominant over 5%. Dominant species included Actinocyclus ehrenbergii, Coscinodiscus curvatulus, C. divisus, C. jonesianus, C. radiatus, C. rothii, C. subtilis, Cyclotella stylorum, Epithemia hyndmanii, Hydrosera whampoensis, and Trachyneis aspera. Diatom abundance varied spatially, with the absolute abundance of diatoms ranging from 13 valves/g to 11×104 valves/g, and averaging 2.5×104 valves/g. A canonical correspondence analysis (CCA) was used to explain the relationships between diatom distribution and sediment properties in the Minjiang Estuary. CCA revealed that the major elements (Fe2O3, Na2O, CaO, MgO, TiO2, SiO2, Al2O3, and K2O) were closely related to diatom abundance. Four diatom assemblages were distinguished, representing different sediment properties, which may assist late Quaternary palaeoceanographic reconstructions of the Minjiang Estuary.