The composition of the microbial communities of the mesopelagic and bathypelagic regions of the central and south Adriatic Sea was analyzed in this thesis. The abundance of viruses, heterotrophic bacteria, heterotrophic nanoflagellates, and cyanobacteria (Synechococcus and Prochlorococcus) were analyzed. The viruses to bacteria ratio, bacterial production, and the share of High Nucleic Acid (HNA) and Low Nucleic Acid (LNA) groups within the heterotrophic bacteria were determined. Concentrations of dissolved O2, NO3, PO4, SiO4 and Chlorophyll a were determined, as well as measurement of temperature and salinity as the most important abiotic factors. Viral abundance in the investigated area ranged from 1.83 ± 1.54 x 106 VLP mL-1 to 12.19 ± 2.73 x 106 VLP mL-1, and the number of viruses on average was 22.3 times higher than the number of heterotrophic bacteria at all stations. The number of viruses was significantly affected by heterotrophic bacteria and heterotrophic nanoflagellates, while the other measured parameters had minor significance for the number of viruses.