Population dynamics of the planktonic diatom Pseudo-nitzschia pungens was investigated at the Zhelin Bay, China, between May 2000 and December 2004. Monthly or seasonal plankton samples were collected from nine stations along the inner to outer bay gradient. Among the 1045 samples collected, P. pungens on average accounted for 2.9% of the total phytoplankton cells, with densities ranging from 0 to 50.94 × 104 cells l−1 and a grand mean of 1.43 × 104 cells l−1. Two hundred and fourteen samples (20.5%) had densities of P. pungens above 104 cells l−1 and 40 samples (3.8%) had densities that were above 105 cells l−1. Results of the grey incidence–regression analysis show that water temperature, zooplankton and salinity were the most important among the 13 environmental factors influencing population density of P. pungens. Water temperature has a highly significant linear relationship with the population density, with 23.8°C or higher being an essential condition for the algal bloom. Grazing by zooplankton was probably the most important factor controlling the algal bloom. With continued decreasing of richness and organism size of the zooplankton community at the Zhelin Bay, P. pungens blooms may become more frequent. The bay has a large-scale mariculture operation, therefore it is important to carefully examine and monitor the potential impacts of toxin-producing P. pungens on human health as well as ecosystem health of the bay.