Abstract: The comparison of the predominant bacterial community structure in the gastrointestinal walls between Lutjanus sebae (Cuvier, 1816) and Ephippus orbis (Bloch, 1787) based on 16S rDNA PCR2DGGE fingerprint using a culture independent method was conducted in the paper. The results showed that abundant bacteriumwere planted in the gastrointestinal walls of both marine finfish species, the similarity was above 50% in the community structures in the gastrointestinal walls with the highest similarity of 67% in the bacterial composition between the intestinal wall of Lutjanus sebae and that of Ephippus orbis, and the walls of the stomach and the intestinal in one fish shared the same most predominant bacteria species, which might reflect the same aquaculture environment and the diet fedfor bothfinfish species. However, the difference of the richness and relative abun dance in the bacterium of the gastrointestinal walls in both finfish species was also observed from the DGGEfingerprint with the results of richer bacterium of the gastrointestinal wall in Ephippus orbis compared to that in Lutjanus sebae, which might due to the different natural living habits. The first time of the establishment and comparison of the 16S rDNA2DGGEfingerprint in the gastrointestinal wall of marine finfish in present study do help to elucidate the microflora structure in the gastrointestinal wall of marine finfish.