Threats to the marine habitats and sea biodiversity is a global issue caused mainly by human influence. Overfishing of commercial sea organisms, degradation of marine habitats, sea pollution, invasive species and global climate changes are main threats to the sea environment. In order to successfully manage the Adriatic Sea and plan for the protection of selected marine habitats and species it is necessary to list, chart and specify their level of endangerment. Main subject of this thesis is to list habitats and pertaining flora and fauna at 20 stations inside protected (National park Brijuni, Nature park Kamenjak) and unprotected areas in Istria. A total of 376 species were recorded within 10 biocenosis. Stations inside of NP Brijuni are least affected by anthropogenic influences, and the largest wealth of fish species is found in this area. The greatest threat to all the investigated stations is the excess of organic matter in the water column causing the constant algae blooms that are later depleted as a mucus on the seabed. Along with all the investigated stations, discarded solid waste from the anchored boats was observed. There were also many fishing gears found. Boat anchoring is also a major problem for marine habitats at all research stations. The invasive ctenophore Mnemiopsis leidyi Agassiz, 1865 were found on all investigated stations of western and southwestern Istria. Gathered data from this thesis will be used for further monitoring of marine habitats, sea management strategy and evaluation of possible negative anthropogenic influences.