Abstract: In this study we investigated the diversity and stability of the bacterial community structure in the juvenile (before the migration) and adult (after the migration) Coilia nasus using PCR-DGGE. The DGGE fingerprint bands were abundant and there were 70 detectable bands with different signal intensities. The number of bands in the water (28) was higher than that in the gill, the stomach, the intestinal wall, and the intestinal contents of Coilia nasus before and after the migration. And the numbers of the bands in the tested organs in adult Coilia nasus were higher than those in juvenile Coilia nasus. The UPGMA clustering and PCA analysis of the DGGE fingerprint showed significant differences between samples. Between the water sample and the post-migration Coilia nasus, the similarities of the bacteria structures in the fish gill, the stomach and the intestinal contents were only 43%, 35% and 28% respectively. Forty-three DGGE bands were successfully cloned including -Proteobacteria (25.6%), -Proteobacteria (7%), -Proteobacteria (16.3%), Actinobacteria (25.6%), Firmicutes (9.3%), Bacteroidetes (7%), Tenericutes (4.6%), Chloroflexi (2.3%), and some unclassified bacteria (2.3%). These results revealed that the bacterial community varied significantly at different migration stages, and in different bacterial parasitic parts of Coilia nasus. Therefore the external environment and the host should be the main factors affecting the composition of a bacterial community.