The importance of aquaculture is continually increasing in the food-producing sector, and one of the most farmed fish in Adriatic Sea is European seabass (Dicentrarchus labrax). Antibiotics are used for treatment of diseased fish in aquaculture, thus contributing to the spread of antibiotic resistance among environmental bacteria. The aim of this paper is to compare microbial communities between two fish farms, one which uses antibiotics for treatment and the other one which holds antibiotic-free certificate. Skin microbiome is highlighted due to the role of skin in defense against pathogens. Samples were collected during summer from two fish farms, near island Cres and near island Vrgada. Physico-chemical analysis of seawater was performed, as well as microbiological analysis of skin swabs, seawater and sediment. The antibiotic susceptibility test and bacterial DNA extraction were also performed. Bacteria identification was performed with determining the nucleic acid sequence of 16S rRNA gene amplified in polymerase chain reaction (PCR). There were 55 bacteria species identified in skin swabs, seawater and sediment samples. Species were mostly specific to each sample type. Only two bacterial genera, Pseudomonas and Vibrio, were identified in skin swabs samples from both fish farms. There was no statistically significant difference (p < 0,05) in antibiotic resistance of bacterial isolates from skin swabs between two fish farms. Pathogenic bacteria identified in skin swabs were Vibrio alginolyticus, V. anguillarum and V. harveyi, and showed resistance to certain antibiotics. The results indicate a potential problem for fish health management in case of disease outbreak.