Mytilus galloprovincialis Lamarck, 1873 is a species widespread in the Adriatic Sea. Due to its edibleness, it is the most important breeding species of shellfish grown in Europe. Two farms have been registered in the Neum Bay. The paper analyzes populations of M. galloprovincialis from three locations, two from the Neum Bay and one from Mali Ston in Croatia. Sampling was done during May 2019 in the tidal zone. According to the WFD and typology, these three localities belong to coastal waters of polyhialine with fine-grained sediment. According to the average values of physical and chemical parameters and chlorophyll, the 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 valve in 90 individuals (30 per locality) included external parameters (height, total length and width of the shell) as well as total weight, soft tissue weight and shell weight. As the internal parameters, the characteristics of the ligament, retractor muscles and adductor muscles are analyzed. Using statistical analyzes (descriptive statistics, post Hoc analysis and correlation), differences in the total weight, length and parameters of the adductor and retractor muscles have been determined. The species from Mali Ston are discriminated 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 for monitoring the state of the populations. Along with genetic analysis, it can be used for monitoring changes in the environment. Determining pathogens in mussel species in Croatia, Slovenia and Italy is an example of controling the conditions of natural and breeding species using various methods and analyses.