Mytilis galloprovincialis Lamarck, 1873 is a species widespread in the Adriatic Sea. Due to the its edibility, it is the first shellfish breed in Europe, and two farms have been registered in the Neum Bay. The paper analyzes native mussel populations of M. galloprovincialis from three populations (Neum Bay two and Mali Ston Croatia). For the purposes of the analysis, sampling was performed in the tide zone in May 2019. According to the WFD and typology, these three localities are in the type of coastal waters of polyhialine with fine-grained sediment. According to the average values of physical-chemical and chlorophyll, Neum Bay is in the category of good ecological status, while Mali Ston is stated to be a reference site. Morphometric measurements of the right eyelid in 90 individuals (30 per locality) included external parameters (height, total length and width of the shell) as well as total weight, gut weight and shell weight. As the internal parameters, the characteristics of the ligament, retractor muscles and adductor muscles are analyzed. By the application of statistical analyzes (descriptive statistics, post Hoc analysis, correlation and descriptive statistics), differences in the total weight, length and parameters of the adductor and retractor muscles have been determinated. The species from Mali Ston are clearly separated from the species of the Neum Bay, which indicates more pronounced anthropogenic influences in the areas of the Neum town. Morphometric analysis is a powerful tool in monitoring the state of populations and in combination with genetic-molecular analysis can indicate changes in the environment. Determining pathogens in mussel species in Croatia, Slovenia and Italy is an impulse to control the condition of natural and breeding species, using various methods and analyzes.