水库在我国东南沿海地区是重要的饮用水水源地,对地区经济发展和社会稳定起到重要作用.选择亚热带地区典型的热分层水库——福建莆田东圳水库,于2011年秋季稳定分层期,以水体温度的垂直变化特征为依据进行分层采样.应用PCR-DGGE和克隆测序的方法研究浮游细菌群落的垂直分布特征,利用多元统计分析揭示细菌群落与热分层水体理化指标之间的关系.结果显示:溶解氧、电导率、叶绿素a、总氮、氨氮及硝氮在上下层水体中的分布有显著差异,下层缺氧区细菌的Shannon-Wiener指数和DGGE条带数明显高于上层好氧区,表明东圳水库热分层水体中存在明显的物理、化学及生物分层现象.测序结果表明β-变形菌可能是东圳水库中占优势的细菌类群,统计结果提示溶解氧是显著影响细菌群落组成的环境因子.热分层水体的物理化学分层与水体细菌群落结构密切相关,提示水库生态学研究应对水体热分层给予重视.;Fujian reservoirs in southeast China are important water resources for economic and social sustainable development, although few have been studied previously. Dongzhen Reservoir, a typical subtropical stratified reservoir in Fujian, was chosen for investigation of bacterial distribution, composition and diversity in autumn 2011. As the only built large reservoir in Putian City, it plays an important role in irrigation, flood control, hydroelectric power, and water supply. Dongzhen Reservoir shows an obvious phenomenon of water thermal stratification during summer and autumn, thus creates a unique gradient of environmental variables along the water column. We investigated the bacterial community and its relation to environmental variables in this study for a better understanding of vertical distribution of bacterial community and the primary environmental drivers in a stratified reservoir. Five water samples were collected from five different depths according to the vertical changes of temperature. Both PCR-DGGE and sequencing were used to investigate the bacterial community and diversity. Moreover, physical and chemical parameters were measured according to the national standard methods. Multivariate statistical techniques were used to examine the relationship between bacterial community and environmental variables. Principal component analysis (PCA) clearly showed that water temperature, dissolved oxygen (DO), chlorophyll a (Chl a), total nitrogen (TN), ammonia nitrogen (NH<sub>4</sub>-N), nitrite/nitrate nitrogen (NO<sub><em>x</em></sub>-N) and electric conductivity of the upper aerobic zone were differed from those of the deeper anoxic zone. Both the number of DGGE bands and the Shannon-Wiener index of the deeper anoxic zone were higher than those of the upper aerobic zone. Further, two groups were distinguished by the cluster analysis of bacterial communities based on the Bray-Curtis similarity. Thus, Dongzhen Reservoir presented an obviously physical, chemical, and biological stratified phenomenon. Seven bands that common to all sampling depths were extracted and sequenced, and among which four were identified as Betaproteobacteria, indicating that Betaproteobacteria were the most dominant taxa in Dongzhen Reservoir in autumn. Bacterial community composition and diversity differed greatly among different sampling depths, and these differences were closely related to the physical and chemical stratification of the water body. Redundancy analysis (RDA) demonstrated DO was the significant environmental variable that shaping the bacterial community and diversity (<em>P</em> < 0.01). Therefore, we should pay more attention to DO and thermal stratification of reservoirs for sustainable reservoir management.