In order to study the correlation between microbial diversity and the pollution degrees of the ruraldrinking water in Dongjiang River basin. Five types of drinking water of this basin were collected,and fifteen water samples of five types of drinking water of this basin had been collected from reservoir,centralized water supply wells,wells in the vicinity of pig farms,wells nearby embankment and wells in villages. The six(physical,chemical,and biological) property indices of water samples were tested,at the same time,the DGGE analysis was done. The results of PCR-DGGE fingerprint indicated that bacterial richness of these drinking water samples were high,and different samples in fingerprint were different distinctively. The UPGMA dendrogram of sample basis on DGGE fingerprints showed the structure of different types of bacteria in drinking water in rural communities is obvious differences. And the results of CCA showed that the concentration of phosphorous has the largest relevance to the community structure of bacteria in water samples,followed by the concentration of nitrogen in the water. Ten typical bands were excised and sequenced. The sequences obtained were affiliated with Spirochaetes,Cyanobacteria,Proteobacteria,Actinobacteria,Acidobacteria.