To know the microbiome composition and the relationship among Coilia nasus and living area,the preliminary analysis of the bacterial community structure in the water environment,gill,stomach and intestine of Coilia nasus from fishponds,including intestinal wall and intestinal contents based on 16S rDNA PCR-DGGE figure using a culture independent approach.Results indicated that bacterial community structure could be analyzed by PCR-DGGE,The DGGE fingerprint showed respectively 27,9,13,19,18 obvious different Signal strength bands in the samples of water environment,gill,stomach,intestinal wall and intestinal contents of Coilia nasus,meanwhile,the Shannon diversity index of which respectively were 3.037,1.883,2.193,2.825,2.683,these might reflect the existence of rich bacteria species.The clustering analysis to the DGGE fingerprint displayed that no significant differences between groups of Repeating sample,the similarity of which above 95%; The sample of gill and stomach of Coilia nasus get together for a branch,the bacteria structure similarity of which was 77% and that in the intestinal wall and intestinal contents of Coilia nasus was 38%.42 DGGE bands were all successfully re-amplified,cloned,sequenced and aligned with BLAST,including Proteobacteria,Actinobacteria,Firmicutes,Tenericutes,Bacteroidetes Cyanobacteria,Fusobacteria and some unclassified bacteria.These comparison analyses reveal that the great amount of bacterial community in Coilia nasus derived from the culture water.DGGE technique could be used to analyze the bacterial genetic diversity and clarify the predominant bacterial community of Coilia nasus from ponds and its environment.This research has contributed to the development and utilization of probiotics and disease control.