Description: Sediment bacterial community and their relation with environmental factors were investigated in the five different trophic status lake regions sediment, Meiliang Bay, Wuli Lake, Gonghu Bay, Western Lake Taihu and Xukou Bay in a large, shallow, eutrophic freshwater lake (Lake Taihu, China). Water and surface sediment samples were collected at 35 sampling sites in January 2014 (winter) and July 2015 (summer). The physicochemical characterization showed that there were obvious changes in the trophic status and eutrophic index of five lake regions, which was mainly due to the difference of organic matter source. Based on the analysis of aquatic environmental characteristics, the organic nitrogen or nitrate nitrogen was the main storing form in the overlying water of five lake regions. In addition, nitrate nitrogen in pore water was lower than in overlying water, while ammonia nitrogen in pore water was higher than in overlying water. According to the DGGE profiles, temporal and spatial variations of bacterial community were apparent. Bacterial diversity was higher in summer than in winter and increased with the decrease in the lake region trophic status. The dendrogram of the bacterial community similarities revealed that samples were almost all grouped into two defined clusters (summer and winter), which indicated that season rather than region was the dominant factor. Canonical correspondence analysis demonstrated that ammonia nitrogen and nitrate–nitrite nitrogen in the sediment and pore water, organic matter and temperature significantly influenced the sediment bacterial community in the five lake regions.