Abstract: In the present study, the sample of intestinal contents of Elopichthys bambusa which was feed by artificial diet and ice fish was collected to construct PCR-DGGE fingerprinting, the population structure and the diversity of intestinal bacteria in Elopichthys bambusa was investigated by cloning and sequencing the purposes binding strips. The DGGE fingerprints of intestinal contents showed that 21 and 17 bands were observed from Elopichthys bambusa which was feed by artificial diet and ice fish; through BLAST comparison, the sequencing results revealed that the similarity between sequencing gained and GenBank was 98%100%. The representative species of Elopichthys bambusa which was feed by artificial diet were Weissella koreensi, etc. And the representative species of Elopichthys bambusa which was feed by ice fish were Moellerella wisconsensi, etc. From the similarity of lanes and bands, there were more significant difference between intestinal bacteria in different Elopichthys bambusa culture pattern, and the similarity was 11.9%42.6%. The highest band H' index in DGGE fingerprint of Elopichthys bambusa intestinal bacteria was the fifth set of samples which was feed by artificial diet, and to 2.84, the lowest was the sixth set of samples which was feed by ice fish, and under 2.46. The results of this study suggested that, feeding artificial feed and iced trash fish affected the composition of fish intestinal microflora, and this provided basic references to diets development. Furthermore, the PCR-DGGE fingerprinting of intestinal bacteria in two types of Elopichthys bambusa was benefit to product tracking and probiotics research.