Our objective was to evaluate the effects of fish meal (FM) replacement with defatted silkworm pupae (DSP) on the intestinal bacterial community structure in Jian carp () using culture-independent 16S rDNA PCR-DGGE fingerprinting. Five isonitrogenous (36.8% crude protein) and isoenergetic (5.5% crude lipid) diets were formulated as follows: one basal diet with 10% FM (DSP0), three diets with 25%, 50%, and 75% FM replacement (DSP25, DSP50, DSP75), and two FM replacement diets (DSP50 and DSP 75) that were supplemented with 0.7% crystalline lysine (DSP50-Lys, DSP75-Lys). A total of 324 juvenile Jian carp (mean body weight: 15.30±2.97 g) were randomly assigned to one of 6 groups (3 replicates per group, 18 fish per replicate). A PCR-DGGE fingerprint analysis revealed that DSP0, DSP25, DSP50, DSP50-Lys, DSP75, DSP75-Lys had bands, respectively. The dominant bacteria were represented by 1The similarity coefficient between the DGGE fingerprint of DSP0 bacteria and the other groups was 50.7%, 50.6%, 69.0%, 42.4%, and 66.7%, respectively. The major bands were recovered, cloned, and sequenced, yielding 19 sequences.The sequences were analyzed by comparison with the NCBI database. The bacterial community consisted primarily of Actinbacteria, Gammaproteobacterial, Cyanobacteria, Bacteroidetes, and Fusobacterial, and included 15 sequences that were uncultured. In conclusion, replacement of graded dietary fish meal protein with defatted silkworm pupae meal had a the intestinal bacterial community structure in Jian carp. However, the addition of lysine reduced this effect. Our results provide a foundation for further development of alternative carp feeds.