Infecting to Melissococcus plutonius, the primary cause of the European foulbrood (EFB) disease, can be followed by infecting to the secondary bacteria, such as Enterococcusfaecalis and Brevibacillus laterosporus. The aim of this research was to diagnose EFB disease by tracking the causes of the disease in apiaries all over Iran. From 260 apiaries, honey bee samples were randomly collected. After samples preparation, the genomic DNA was extracted and specific primers were selected for interested bacteria. Using the conventional polymerase chain reaction (PCR) method for E. faecalis and B. laterosporus and nested-PCR method for M. plutonius, the target fragments were amplified. Desired standard bacteria and distilled water were used as positive and negative controls, respectively. Results showed that out of 260 samples from apiaries, 74 and three samples were positive for E. faecalis and B. laterosporus bacteria, respectively. Also, the results of nested-PCR showed that 58 samples were positive, of which only 12 samples were positive in the evaluation of E. faecalis. Results demonstrated that the highest and the least levels of the infection for M. plutonius and E. faecalis were in the south and east of the country, respectively. Results indicated that sometimes due to the excessive growth of secondary bacteria, the main bacteria can be removed from the environment. Also, findings proposed that those provinces with higher number of populations, followed by higher amount of air pollution, had more infected samples than others. [ABSTRACT FROM AUTHOR]