Abstract: Polyphosphate accummulating organisms (PAOs) play an important role in the phosphorus metabolic cycling in the sediment of reservoir. We assessed the diversity and community structure of PAOs in the sediments by T-RFLP and clone sequencing which targeted ppk1 gene at the hearts of three reservoirs (Jiulongjiangxipi reservoir, Sanshiliujiao lake reservoir and Dongyaxi reservoir) in Fujian Province. The results showed that the diversity of PAOs varied among different reservoirs, though not statistically significant. The diversity of PAOs in the Sanshiliujiao lake reservoir was highest (Shannon index H=2.89±0.03, Simpson index D=0.06±0.01). The community structure of the PAOs in the Sanshiliujiao lake reservoir was most complicated, consistent with the results of the T-RFLP. The differences of dominant PAOs genera in three reservoirs were distinct, mainly concentrated in the Proteobacteria, Actinobacteria and Acidobacteria. The percentage of those three phylum accounted for 74.5%, 85.0% and 75.0%, respectively, of the total PAOs. The dominant groups in each reservoir sediment were Anaeromyxobacter and Solibacter. Various forms of phosphorus had certain influence on the diversity of PAOs. There were significantly correlation between Fe/Al-P and PAOs diversity and community structure. The dominant genus in the three reservoirs, Anaeromyxobacter, was positively correlated with all forms of phosphorus and significantly correlated with insoluble phosphorus such as OP and Ca-P, while Solibacter was negatively correlated with all forms of phosphorus. The results suggested that PAOs had important impacts on the phosphorus cycle of sediment in eutrophicatied reservoirs.