Nosemosis is a significant worldwide disease that can cause severe colony and economic losses by reducing adult honeybees' average lifespan, pollen collection, and productivity. This study was carried out in 11 different districts of Aydın Province, where migratory beekeeping activities are widespread, in the preharvest period between 2018 and 2020 to detect the presence of Vairimorpha (Microsporidia: Nosematidae) species in the region and to identify the causative species. A total of 560 colonies was sampled from apiaries belonging to 56 different beekeepers. In the apiaries, a minimum of 6 colonies, or 10% of the total bee colonies, was selected through a random process for spore quantification. By microscopic examination, samples collected from 35 of 56 apiaries in Aydın districts were positive for Vairimorpha (62.5%) spores. All positive samples were recorded as Vairimorpha ceranae with an amplicon size of 218 base pairs. The sequence results of this study's isolated samples showed very high-level (98–100%) homology with V. ceranae sequences collected that were deposited in the GenBank database. The existence of infection among honeybees, coupled with the molecular identification of the species and the quantification of contamination levels in neighboring apiaries, can elucidate the extent of economic losses attributed to this issue. In addition, for a more comprehensive understanding of the emergence of infection, its prevalence, and the distribution of causative species, it is of great importance in future studies to evaluate and analyze environmental and nonenvironmental variables, including factors such as altitude and temperature of the beehive.