Bats are known to inhabit both caves and open space areas. Bulgaria is among the Еuropean countries with the highest number of bat species. The species found in the country are distributed over a wide area. They range from the Pyrenees and the British Isles to the Pacific region and the Far East. Many bat species are carriers of potential human pathogens. Bats play an important role in agriculture and act as a biological pest crop control agent. Bulgarian bat ecosystem comprises temperate climate and a wide range of abiotic factors, including humidity, darkness, sunlight, and temperature variations. The metabolism of bats and their body temperature vary significantly between the period of activity and the hibernation. Fluctuations in body temperature can potentially impact host microbiome biodiversity. Temperature variations may induce a high level of microbial mutagenesis. Additionally,the existence in large, mixed-species colonies, togeteher with a relatively long individual lifespan (4 – 16 years) and extensive travel distances, enhances the likelihood of encountering multiple pathogens in a single host organism. This, in turn, facilitates genetic variations and re-combinations among those microbial pathogens, thereby raising their potential to breach species barriers. In this review, we summarized and analyzed the available scientific information concerning the potential microbial human pathogens associated with bats, alongside with our preliminary data on the biodiversity of bats blood microbiome. Future research should focus on bats as both pathogens carriers and dynamic models for predicting emerging and re-emerging zoonotic diseases.