Abstract: Estuary ecosystems are important water sources with microorganisms as key components playing crucial roles in global biogeochemical cycles. However， the spatiotemporal variation in the distribution and abundance of microbes as well as the response to anthropogenic environmental changes are still poorly understood. In this study， seven sampling sites were selected in Jiulong River estuary， which has experienced intensive human perturbation in recent years. The changes in the diversity and structure of microbial community were analyzed while the environmental factors were determined both in rainy and dry seasons. The results of 16S rRNA gene clone libraries indicated that Proteobacteria， Actinobacteria and Bacteroidetes were the most predominant groups. Both in rainy and dry seasons， the ratio of Proteobacteria to Actinobacteria was about 2∶1～3∶1 in the upper reaches while about 1∶1 in the lower reaches. At the level of class， Betaproteobacteria dominated the phylum of Proteobacteriain in the upper reaches but Alphaproteobacteria were the majority in the lower reaches. Firmicutes were the fourth abundant group in dry season， implying the contaminated water bodies by fecal pollution. Our study demonstrated that the microbial community in Jiulong River estuary was sensitive to humancaused environmental changes and displayed a distinct spatiotemporal pattern driven by salinity， nutrients， temperature， river flow and contamination such as animal feces．