Dinaric limestone cave systems, recognized as a hotspot of subterranean biodiversity, inhabit composite microbial communities whose structure, function and importance to ecosystems was poorly considered until the last few years. Filamentous microbial biofilms from three caves in Dinaric karst were assessed using 16S rRNA-based phylogenetic approach combined with universally protein coding genes/proteins. Studied clone libraries shared divisions but phylogenetic distribution of the obtained phylotypes differed: in Veternica and Vjetrenica clone libraries, Nitrospirae prevailed with 36% and 60% respectively, while in Izvor Bistrac the most abundant were Alphaproteobacteria (41%) followed by Firmicutes (32%). Moreover, three phylotypes were associated with novel uncultured candidate divisions OP3, WS5 and OD1 revealing the diversity and uniqueness of the microbial world in caves. Deeply understanding subterranean habitats could elucidate many new aspects in phylogeny and evolution of microorganisms as well as animal taxa, adjacent to their energy suppliers in microbial communities and biofilms.