The present study explores the gut microbiota of Apis mellifera and Apis dorsata using Next- Generation Sequencing (NGS) to understand microbial diversity and relative abundance. A total of 05 specimens of each honeybee species were collected from District Kasur, Pakistan, and processed under sterile conditions for gut dissection. DNA was successfully extracted, and by V3-V4 region of the 16S rRNA gene was successfully amplified. The analysis revealed significant bacterial phyla, with Proteobacteria dominating both species, accounting for 83% in Apis mellifera and 80% in Apis dorsata. Furthermore, prevalent phyla, including Bacteroidota, Firmicutes, and Actinobacteriota, were documented. Prominent genera identified in both species were Commensalibacter, Dysgonomonas, Lactobacillus, and Gilliamella, which contribute to gut health and fermentation processes. Differences were observed in the dominance of families with Enterobacteriaceae prevalent in Apis mellifera and Acetobacteraceae in Apis dorsata, potentially linked to diet and habitat. The findings suggest that variations in gut microbiota are shaped by environmental conditions, foraging behaviors, and evolutionary differences between these two species. These results provide baseline information for future research into the functional roles of microbiota in honeybee health and ecological adaptation.