Objectives In this study, the gut microbiome of healthy adult honeybees,Apis cerana, was investigated by sequencing the V3 - V4 region in 16S rRNA gene using Illumina Miseq platform. Results The total of 37,853 reads for 16S rRNA gene were obtained and 30,121 (79.6%) reads were valid with 25,291 (84.0%) reads that were classified into 116 species belonging to four major phyla. The relative abundances of the bacterial isolates in honeybee samples were phylumProteobacteria(70.7%),Actinobacteria(10.7%),Firmicutes(10.3%), andBacteroidetes(8.4%), respectively. Lactic acid bacteria comprised 18.95% with 10 groups includingBifidobacterium asteroides,B. indicum,Fructobacillus fructosus,Lactobacillus apinorum,L.apis,L.helsingborgensis,L.kimbladii,L.kullabergensis, andL. kunkeei. Conclusions The presence of beneficial bacteria in the gut highlighted their role in the honeybee and suggested that they can be promising candidates for the development of probiotics for health improvement, infection control and disease management of honeybees.