The distributions of culturable bacteria and functional bacteria associated with nitrogen (N) or phosphorus (P) in the backwater areas of the Three Gorges Reservoir (TGR) were investigated. Results from seven locations in the TGR indicated that the abundance of total bacteria was high, with 8.12 x 10(6), 2.70 x 10(7), and 6.73 x 10(10) colony-forming units per milliliter or per gram dry weight in surface water, bottom water, and sediments, respectively. Aquatic environments with higher nutrient loadings possessed higher bacteria densities and lower bacteria community diversities. Eight kinds of functional bacteria ratios, including surface water to bottom water and ratios of water to sediments, were calculated, in which four kinds of functional bacteria, namely, nitrogen-fixing bacteria, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and organophosphate-solubilizing bacteria, displayed obvious differences in different locations. Based on the functional bacteria ratios of water to sediments, it was found that the obtained result of location grouping from cluster analysis was similar to that based on the community-level physiological profiles studies. The above results showed that the ratios of functional bacteria could distinguish the aquatic environments with different trophic conditions in the TGR. This demonstrated that the distribution ratios of functional bacteria in aquatic environments could work as potential bioindicators to reflect the trophic condition of the water.