We assessed the complexity of bacterial communities occurring in the digestive tract of the Japanese honeybee, Apis cerana japonica, using histological and 16S rRNA gene sequence analyzes. Both Gram-positive and -negative bacteria were observed, and the number of gut bacteria was higher in old larvae compared with young larvae. A total of 35 clones were obtained by a culture-dependent method, and 16S rRNA gene sequence analysis revealed that the bacterial population in the gut of Japanese honeybee was diverse, including the phyla firmicutes, actinobacteria, and alpha-, beta-, and gammaproteobacteria. Further investigation by in vitro inhibition assays was carried out to determine the ability of an isolate to inhibit Paenibacillus larvae, the causal agent of American foulbrood. Out of 35 isolates, seven showed strong inhibitory activity against P. larvae. Most of the antagonistic bacteria belonged to Bacillus species, suggesting that the bacterial isolates obtained in this study appear to be potential candidates for the biological control of P. larvae.