Abstract: An investigation in August 2013 on phytoplankton and environmental factors was carried out in the southern waters of Miaodao Archipelago.Shannon-Wiener index, evenness index and richness index were used to analyze species composition, distribution of biodiversity of phytoplankton and dominant species in the southern waters of Miaodao Archipelago.A total of 41 taxa were found, among them 21 taxa were diatom and 19 taxa were dinoflagellate.Diatom and dinoflagellate were the main part of the species composition.The average number of species at each station ranged from 2 to 17.We found that the values of the number of species, Shannon-Wiener index, richness index and evenness index in surface waters were higher than those in bottom waters.The chemical oxygen demand (COD), chlorophyll a (chlorophyll-a) and total phosphorus (TP) had great effect on the number of species and richness index in summer, using Pearson correlation analysis based on the number of species, Shannon-Wiener index, richness index, evenness index and environmental factors.The results of ABC curves showed that the moderate disturbed stations were focused on the bottom of the waters and concentrated in the Miaodao Strait in summer.