Abstract: To clarify the community structure and diversity of larval gut bacteria in Carposina sasakii and Grapholitha molesta, the V4 regions of the 16S rDNA genes of intestinal bacteria of C. sasakii and G. molesta larvae which fed by golden delicious apple, were amplified and sequenced by Illumina HiSeq technique. The results showed that a total of 229043 high quality reads of gut bacteria in C. sasakii larvae were obtained and clustered to 2112 OTUs, which were annotated into 27 phyla, 65 classes, 124 orders, 205 families and 281 genera. 240389 reads of G. molesta were produced and clustered to 957 OTUs, which were annotated into 22 Phyla, 46 Classes, 89 Orders, 145 Families and 180 Genera. C. sasakii was dominated by the Proteobacteria (87.98%±5.29%), Firmicutes (3.91%±1.19%), Actinobacteria (1.04%±0.47%), and G. molesta was mainly dominated by Proteobacteria (50.06%±19.56%), Firmicutes (32.02%±8.48%) and Cyanobacteria (25.24%±10.28%). All of Phylum, Class, Order, Family, Genus, Species of the bacteria were significantly different between C. sasakii and G. molesta. Those results suggested that the gut bacteria community in these two fruit-boring pests was notably different, although they were both fed by apple fruit. The bacteria communities were more complex in C. sasakii than in G. molesta, which might account for different feeding and digestion mechanisms. The results could lay a foundation to reveal the association of the intestinal bacteria with these two fruit borers.