Abstract: The distribution and size-fractional Chl a concentration (>20 μm, 2~20 μm, < 2 μm) in Qinzhou bay were studied in March (dry season) and July (wet season), 2014. Dissolved inorganic nitrogen concentration and N/P ratio were both high in the two seasons, whereas soluble reactive phosphorus concentration in dry season was higher than wet season. Chl a concentration and size structure were significantly different between two seasons. The Chl a concentration in dry season (1.70±0.74 μg/L) was significantly lower than in wet season (7.81±3.63 μg/L) (p < 0.01). The dominant size fraction was transformed from nano-phytoplankton (51.8±14.0%) in dry season to pico-phytoplankton (50.4±17.4%) in wet season. The high concentration of Chl a in wet season was contributed by pico-and micro-phytoplankton. Concentration of Chl a which contributed by nano-phytoplankton was not differ significantly between two seasons, however, their contributions to total Chl a concentration was declined from 51.8±14.0% in dry season to 15.5±9.2% in wet season. According to the results, runoff input, the change of nutrient concentrations and high density of oyster cultivation were considered to be the major factors leading to the change of phytoplankton size structure in Qinzhou bay.