Abstract: Seasonal distribution of chlorophyll-a and its relationship with environmental factors and primary productivity were investigated during the period from May 2006 to February 2008 in waters of the Pearl River Estuary.Results show that no significant difference was observed between chlorophyll-a contents in the surface layer,in the sublayer and in the upstreams;chlorophyll-a content in the surface layer was found to be obviously higher in summer and spring than in fall and winter,while no significant difference was observed between sites.A similar trend of the variation of the primary productivity was observed in waters of the Pearl River Estuary.Pearson correlation analysis shows that chlorophyll-a concentration was significantly correlated with phytoplankton cell density and primary productivity.Environmental factors affecting chlorophyll-a content varied sharply with site and season.