A series of samples were collected from four stations located in Nanji Islands National Nature Reserve (NINNR) from April 2006 to March 2007. During this investigation monthly samples were gathered from July 2006 to March 2007, which delineated summer, autumn and winter conditions. During spring, from April to June 2006, a period that Prorocentrum blooms have occurred previously, water samples were collected every week. Both surface and bottom samples were obtained. Species composition, seasonal variations and vertical distribution of Prorocentrum populations as well as several chemical parameters were determined, as well as the connections between Prorocentrum dynamics and water temperature, salinity, nitrogen and phosphorus concentrations. Four Prorocentrum species were found: P. triestinum Schiller, P. donghaiense Lu, P. micans Ehrenberg and P. sigmoides Bohm. Of these, P. triestinum and P. donghaiense were the dominant species, especially in spring. Large blooms were recorded on 12 and 25 May, respectively. During these blooms Prorocentrum abundances at the surface were far greater than at depth. The temperature and salinity values observed when P. triestinum was at its maximal abundance were 18.5–19.5 °C and 29.58–30.95‰. For P. donghaiense they were 18.5–21.3 °C and 29.03–30.92‰, respectively. Higher Prorocentrum abundances were correlated with both lower inorganic phosphorus and nitrogen concentrations. Using correlation analysis, we found that the dynamics of Prorocentrum population had a strong positive correlation with the N:P ratio, and a negative correlation with absolute phosphorus concentrations. Phosphorus concentrations played a key role in the variations of Prorocentrum populations. The nutrient storage capability of Prorocentrum was greater than that of many diatom species, which may explain how Prorocentrum could grow better and bloom under lower nutrient concentrations in NINNR, as well as in the Yangtze River Estuary, Zhejiang coastal waters and East China Sea.