Microsporidia are intracellular parasites infecting a wide range of vertebrates and invertebrates. In bees, they cause a diarrheal disease called nosematosis, which represents a growing problem contributing to the decline of bee colonies. This parasitic disease infects the gastrointestinal tract of bees, disrupts their immune system, weakens them, and shortens their lifespan. There are two known species of this microsporidial parasite with a global distribution: Vairimorpha apis and Vairimorpha ceranae, with current research indicating that the species V. ceranae is gradually replacing V. apis. In this study, we focused on the detection and occurrence of Vairimorpha spp. in bee colonies kept in different environments, as well as on comparing the impact of hive location on its occurrence. The methods used included sampling from winter bee carcasses, microscopic examination of bee gut contents, and subsequent molecular duplex PCR analysis. Altogether, we examined 82 hives located at 4 different sites and focused on the impact of transportation as an abiotic factor disturbing bees leading to the development of Vairimorpha spp. disease. The results indicate an increased occurrence of this parasite in hives located in urban sites and hives situated in intravillage locations, which may be attributed to transportation and associated vibrations as an abiotic stress factor. Detection revealed that all samples were positive for Vairimorpha ceranae.