Honey beekeeping is a large-scale global industry in the world; bee health suffers from one of the most dangerous diseases by Vairimorpha (Nosema) pathogen. The molecular genetic diversity among the collected honeybee populations was investigated using the mitochondrial DNA cytochrome oxidase subunit I (COI). To determine the level of Vairimorpha (Nosema) ceranae (V. ceranae) concentration within honeybee individuals in the colony, we dissected the honeybee and extracted the midgut, ovary from newly hatched virgin queens, and hypopharengeal gland and midgut from newly hatch worker bees. The spores were counted initially using light microscopy. The quality and quantity were determined by conventional PCR and qPCR technology to track infection levels. The sequence of COI showed that belong to Apis mellifera Arabia haplotype by 99% and by 78% to African haplotype Apis mellifera capensis. Vairimorpha ceranae with significant differences ranged from 0.90×10⁶ spore/bee to 18.0×10⁶ spore/bee (samples code C7) for adult bees. While the copies number of V. ceranae varied from one organ to another, the pathogen was in newly hatched workers or virgin's queens higher than old generation. The hypopharengeal glands in new hatch honeybees' workers were the most infected of all organs by 25.49×10⁶ copies. These results demonstrate the importance of maintain proper quarantine measures to reduce infection. Also, these results could explain how V. ceranae pathogen is transmitted vertically and horizontally within and between the colonies.