Apis mellifera, widely farmed around the world, is the most economically important species within the genus Apis. While the microbiota of live honey bees have been extensively examined, bacteria found in deceased honey bees (which might indicate infection or opportunistic pathogens) is in contrast poorly studied. Therefore, we decided to investigate the mesophilic bacterial flora of dead honey bees. So, in September 2013, dead adult worker honey bees were collected from 12 different cities, most of which were in the border provinces of Turkey. We identified bacterial isolates at the species level by using different morphological, biochemical, physical and molecular methods, in conjunction with molecular phylogenetic analysis. We constructed phylogenetic trees for isolated bacteria with the MEGA 6.0 program and neighbor-joining trees were reconstructed based on 16S rDNA gene sequences. The phylogenetic trees indicated that isolates DE003, DE007, DE011, DE001, DE019 and DE016, DE029 could be new members of the genera Erwinia, Acidovorax, Hydrogenophaga and Bacillus genus, respectively. In the bioassay study results, we observed that DE019 Hydrogenophaga sp. (64.7%) and DE004 Klebsiella grimontii (73.3%) had lethal effects on the honey bees. The other mortalities ranged from 10% to 25% (p>0.05), and according to a One-Way ANOVA analysis DE004 and DE019 significantly affect the A. mellifera caucasia in adult worker honey bees. This study is the first report of Hydrogenophaga as honey bee pathogen.