The silkworm (Bombyx mori), a specialist herbivore that feeds on mulberry leaves, is an economically important insect in China. Exploring the bacteria of silkworm intestine and phyllosphere in mulberry leaf is of great significance to reduce silkworm diseases. Taken silkworm larvae on the third day of the fifth instar and mulberry leaves feeding as the research object, the 16S rDNA gene fragments (V3-V4 region) of bacteria in silkworm intestine and phyllosphere of mulberry leaf were sequenced by Illumina MiSeq. The results demonstrated that there was no significant difference (P > 0.05) among the diversity indexes (Shannon index and Simpson index) of bacteria in phyllosphere of mulberry leaf and each particular location in silkworm intestine. NMDS analysis showed that the bacteria in phyllosphere of mulberry leaf and silkworm intestine clustered separately, and there was no significant difference between the bacteria in various parts of the silkworm intestine. Analysis results indicated that the bacteria in the phyllosphere of mulberry leaf and the intestine of silkwormwere annotated into 29 phyla and 268 genera, and four phyla (Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria) were predominant populations. Bacillus, Pantoea and Sphingomonas were the predominant genera in the phyllosphere of mulberry leaf, the foregut of silkworm, and midgut and hindgut of silkworm, respectively. Functional prediction analysis showed that digestive system, immune system, energy metabolism, metabolic diseases and infectious diseases accounted for a higher proportion in the silkworm foregut and midgut, but amino acid metabolism, carbohydrate metabolism, neurodegenerative diseases, immune system diseases, lipid metabolism, metabolism of other