The insect intestinal tract is a complex microecosystem that contains abundant microorganisms. To explore the relationship of the intestinal microflora of lepidopteran insects with host growth, development and disease resistance, we reared silkworm larvae with tricuspid cudrania leaves and mulberry leaves (both belong to the family Moraceae) respectively, used methods of pure culture isolation, 16S rDNA sequence determination and phylogenetic analysis to investigate the gut microorganisms in fourth and fifth instar silkworm in order to find the composition changes of the microbial community that induced by forages. A total of 56 dominant strains were isolated from intestine of silkworm larvae and classified into twelve different genera according to the characteristics of colonial morphology, mycelial, physiological-biochemical identification and 16S rDNA phylogeny. These twelve genera are Brevundimonas, Stenotrophomonas, Enterobacter, Staphylococcus, Pseudomonas, Agrobacterium, Aeromonas, Brevibacterium, Citrobacter, Escherichia, Klebsiella and Bacillus. Only four genera of these dominant strains (Brevundimonas, Stenotrophomonas, Enterobacter and Staphylococcus) were common existence in the intestine of silkworm larvae reared with tricuspid cudrania and mulberry leaves. Besides, five genera of these dominant strains (Aeromonas, Brevibacterium, Citrobacter, Escherichia and Klebsiella) were detected in the intestine of the silkworm larvae which reared with mulberry leaves, while only two genera (Pseudomonas and Agrobacterium) were presented in the intestine of the silkworm larvae reared with tricuspid cudrania leaves. The composition of dominant intestinal microflora had shown significant difference between two kinds of silkworm larvae that reared with different forages. While the silkworm larvae were reared with tricuspid cudrania leaves, it was notable that the diversity of dominant intestinal microflora was considerably lower than that of silkworm larvae which reared with mulberry leaves. In addition, we made preliminary studies on the relationship among different dominant intestinal strains of the silkworm larvae that reared with tricuspid cudrania and mulberry leaves respectively. The certain dominant intestinal strains from silkworm larvae that reared with two different leaves mentioned above were combined together as microbial additive to feed silkworm larvae. Taking 3 independent experiments for each combination, we found that the silkworm larvae got sickness induced by some combinations with the symptoms such as spitting yellow liquid, head shaking and finally led to death within 24 hours. These results suggested that there could be substantial change on intestinal microflora of silkworm larvae, possibly the gut microbial community structure changes, induced by different forages. The composition changes of intestinal microflora were qualitatively differed from the changes of that along with the inter-instar changes of silkworm larvae reared with the same forage. According to the studies, we speculated that the community structure changes and lower diversity of dominant microflora in intestine of silkworm larvae reared with tricuspid cudrania leaves might be related to their retarded growth and susceptibility to Bombyx mori nuclear polyhedrosis virus (BmNPV).