Based on the data collected from the ecological investigation on Guangxi coastal waters in both wet season (September 2009) and dry season (January 2010), the species composition, dominant species, abundance and community diversity of phytoplankton were analyzed. The results showed that a total of 134 species from 40 genera belonging to 4 phyla were identified in the surveyed area. Of all the phyla, diatom was the predominant group, which accounted for 87.3% of the total species. There were 84 common species in both wet and dry seasons and the species similarity index between the two seasons was 81.4%, suggesting no significant seasonal variations in the species composition. During the wet season, there were many dominant species, and the major ones were Chaetoceros curvisetus and Pseudonitzschia delicatissima. The dominant species was relatively simple during the dry season, and Phaeocystis globosa accounted for the absolute majority with a dominance index of 96.1%. The abundance of phytoplankton cells showed significant spatial and seasonal differences. During the wet season, the phytoplankton density decreased from the eastern to western coastal waters, and the density in coastal area was generally higher than that of the offshore waters. In general, the average Shannon diversity index (H′) was 2.79, and the average evenness index (J) was 0.58, suggesting a high diversity of the phytoplankton community. Both H′ and J of phytoplankton showed no clear seasonal variation, whereas the spatial pattern showed an obvious single peak that was higher in central area but lower in the eastern and western areas. Correlation analysis demonstrated that the density of phytoplankton community had definite correlations with environment factors. During the wet season, phytoplankton density displayed a significant negative correlation with water temperature (P<0.05); during the dry season, it showed a significant positive correlation with the dissolved inorganic nitrogen (P<0.01), and significant negative correlations with biochemical oxygen demand (P<0.01) and salinity (P<0.05).