Commercial fish farming is a significant contribution to the provision of high-quality protein food on the Croatian market. Sea bass, Dicentrarchus labrax and gilthead sea bream, Sparus aurata, are the most common species in mariculture, while ciprinides and trout are the most widely cultivated freshwater fish. Since food safety is a basic predisposition for market distribution, the aim of this study was to identify the bacterial microflora of sea bass, common carp and brown trout, Salmo trutta, from commercial farming. Skin and gill swabs were taken over three years throughout the seasons at sea bass farms near Pelješac, carp farm near the Ilova River and trout farm on the Krka River. 70 types of bacteria from 25 genera were detected by the MALDI TOF method. 42 species from 19 genera were found on sea bass, 26 species from 10 genera on carp, and 23 species from seven genera on brown trout. The genera Achromobacter, Aeromonas, Pseudomonas and Shewanella were found in all three fish species. The genera Arthrobacter, Bacillus, Exiguobacterium, Leclercia, Microbacterium, Micrococcus, Pantoea, Photobacterium, Providencia, Psychrobacter, Rhizobium, and Vibrio were found only in sea bass, Enterococcus, Morganella, and Proteus only in carp, and Carnobacterve, Hafnia and Serratia only in brown trout. The results indicate the need for further monitoring of the state of the microbiological flora with the application of good hygiene practice and other measures to reduce the potential harmful impact on farmed fish and human health.

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