Aquaculture of mussels (Mytilus galloprovincialis, Lamarck 1819) by the quantity of production is the most common form of aquaculture in Europe. In Croatia, estimated production is only about 3.000 tonnes of mussels per year. In general, shellfish (including mussels) are considered as a healthy food and their nutritional value is based on a favorable comparison of proteins and fatty acids and the large amount of glycogen. Despite the high nutritive value of food shellfish can pose a danger to human health. The shellfish feeds by filtering large quantities of water, and thus can accumulate different toxic substances like heavy metals as well as microbial pathogens. Among the most important bacterial pathogens that shellfish can accumulate include bacteria of the genus Salmonella, Shigella, Vibrio, Staphylococcus, Pseudomonas, Clostridium, Campylobacter, Yersinia, Aeromonas, Escherichia coli and then a large number of streptococci. Through this work we wanted to determine the presence of different bacterial pathogens in mussels collected at four selected sites in the central Adriatic. Three sites were commercial mussel farms, which in accordance with the microbiological classification of production areas for bivalve molluscs belonging to the microbiological class "A" while on the fourth site of mussels were collected from a commercial fish-farm. The aim was to compare the microbiological quality of the mussels breeding areas (river mouth of Krka, river mouth of Zrmanja and Velebit channel) with mussels collected from the sea bass and sea bream fish-farm (island Vrgada). The paper is intended to determine whether the conditions of multitrophic integrated aquaculture can produce healthy and nutritionally rich animal products. Promotion and development of mussels can significantly increase its production in Croatia in a short time.