Investigation of parasites and diseases affecting molluscs of ecological and economic interest is critical for the management of native stocks and aquaculture. In recent years, much attention has been devoted to investigating the World Organisation for Animal Health listed infectious diseases, so that communities can be prepared to attend public health emergencies and avoid severe income losses. In this context, the health status of Mytilus galloprovincialis Lamarck, 1819 was analysed in two aquaculture sites (Strunjan Bay and Piran Bay, Slovenia), and in four natural mussel beds (Adriatic Croatia International Marinas Pula and Rovinj and St Catherine, Croatia; Marina Koper, Slovenia) along the coast of the northern Adriatic Sea. The mussels were sampled in February and April 2014, and processed for histological examination of several endosymbionts and pathogens that frequently occur in mytilid mussels. Endosymbionts and pathogens were not detected in farmed mussels. Prokaryotic inclusion bodies, the protozoan Nematopsis, Ancistrocoma-like ciliates, haplosporidian-like plasmodia, turbellarian Urastoma cyprinae, and basophilic inclusion bodies were observed in digestive gland cryosections of wild mussels from the coastal region of the northern Adriatic. Fungal spores of Psilocybe sp., Ulocladium sp. and Alternaria sp. were detected between the digestive tubules based on their morphology. Diagnostic PCR did not reveal infection with Marteilia refringens during the studied period, neither in wild nor farmed mussels. We confirmed the site effects on prevalence of infected mussels. Thus, we can conclude that wild areas are more exposed to endobionts and parasites than aquaculture sites.