The present study investigated bacterial pathogens in honey bee colonies, focusing on American Foulbrood diseases and European Foulbrood diseases caused by Paenibacillus larvae and Melissococcus plutonius, respectively. Samples from infected brood, pupa, and combs of Apis mellifera were collected from modern apiaries in Nainital district, Uttarakhand. Three different culture media, i.e., nutrient media, MYPGP media, and KSBHI media, were used to isolate the bacteria under aerobic and anaerobic conditions. Morphological, biochemical, and molecular characterizations (16S rRNA sequencing) of 12 selected bacterial isolates were performed, and the obtained sequences were submitted to NCBI GenBank. The isolates were identified as Enterococcus faecalis, Bacillus tropicus, Bacillus safensis, Bacillus licheniformis, Pseudomonas hibiscicola, Bacillus haynesii, Delftia tsuruhatensis, Bacillus subtilis, Williamsia serinedens, Carnimonas nigrificans, Pseudomonas parafulva, and Bacillus paralicheniformis. The dominant phyla were Firmicutes (58%), Proteobacteria (34%), and Actinobacteria (8%), with Bacillus spp. being the most prevalent. This study highlights the diverse bacterial community associated with honey bee colonies and their potential role in bee health and disease. The study also revealed that the apiaries in the study area were not affected by the pathogens Paenibacillus larvae and Melissococcus plutonius. These findings contribute to understanding the microbial ecology of honey bees and the impact of bacterial infections on colony health.