To date, the microbiome, as well as the virome of the Croatian populations of bats, was unknown . Here, we present the results of the first viral metagenomic analysis of guano, feces and saliva (oral swabs) of seven bat species (,, ,, , and) conducted in Mediterranean and continental Croatia . Viral nucleic acids were extracted from sample pools, and analyzed using Illumina sequencing . The presence of 63 different viral families representing all seven Baltimore groups were confirmed, most commonly insect viruses likely reflecting the diet of insectivorous bats . Virome compositions of our samples were largely impacted by the sample type: invertebrate-infecting viruses were most frequently found in feces, bacterial viruses in guano, whereas vertebrate-infecting viruses were most common in swabs . Most vertebrate-infecting virus sequences were assigned to retroviruses, parvoviruses, iridoviruses, and poxviruses . We further report the complete genome sequence of a novel adeno-associated virus, densovirus and a near complete length genome sequence of a novel iflavirus . Additionally, one of the most interesting findings in this study was the difference in viromes between two contrasting habitats, the continental and Mediterranean Croatia.