In the present work, we investigated the dynamics of the microbial communities in the wedge clam Donax trunculus (Linnaeus, 1758) from the Bulgarian coastal waters of the Black Sea. The samples were collected in the period of January 2020 until December 2022 from Arkutino, Ahtopol, Obzor and Tsarevo. The BIOLOG system was used for microbiological determination. In our investigation were isolated the following microorganisms: Enterococcus cancerogenus, Enterococcus hirae, Escherichia vulneris, Citrobacter farmeri, Acinetobacter gyllenbergii, Enterococcus hirae, Escherichia vulneris, Enterobacter cloacae, Escherichia hermannii, Pseudomonas mendocina, Pseudomonas fulva, Pseudomonas alcaligenes, Pseudomonas putida, Acinetobacter johnsonii, Acinetobacter gyllenbergii, Enterococcus hirae, Escherichia vulneris, Enterococcus gallinarum, Citrobacter sedakii, Pseudomonas putida, Streptococcus lugdunensis, Enterococcus casseliflavus, Vibrio cincinnatiensis, Vibrio alginolyticus, Vibrio parahaemolyticus, Enterococcus hirae, Streptococcus aureus, Staphylococcus lugdunensis and Enterococcus casseliflavus. During the winter period, we detected the presence of Pseudomonas sp. – P. alcaligenes, P. putida, and A. gyllenbergii. In the autumn months we isolated C. sedakii, C. farmeri, A. gyllenbergii, A. johnsonii, P. fulva and E. casseliflavus. In the spring, E. cancerogenus, E. hirae and Pseudomonas mendocina were found. During the summer, the highest biodiversity of microorganisms - E. hirae, E. vulneris, E. cloacae, E. gallinarum, P. putida, V. cincinnatiensis, V. alginolyticus, V. parahaemolyticus, S. aureus, E. hermannii and S. lugdunensis were registered. Although our three-year research showed that some species are permanent and others are transient, we tend to accept the conclusion that there is only a transient microbiota in mussels and it changes depending on environmental conditions or is a result of pollution of the Black Sea.