In this study, Mediterranean mussels (Mytilus galloprovincialis Lamarck, 1819) were collected from the most important mussel distribution/fishing areas in Turkish coastal waters (Canakkale, Balikesir, Izmir). The presence of parasite was investigated based on molecular methods. Molecular identification of parasite species was established by designing parasite-specific primers for PCR amplification and resulting nucleotide sequences were analysed. As a result of this study, four parasite species were identified as Mytilicola intestinalis Steuer 1902, Mytilicola orientalis Mori 1935, Urastoma cyprinae Graff 1882, Parvatrema duboisi Dollfus 1923 respectively. All identified species were found in Izmir (Agean Sea) specimens while Urastoma cyprinae and Parvatrema duboisi were found only in Canakkale (Dardanelle) and Balikesir (Marmara Sea) specimens. Nucleotide composition, pairwise genetic distance and phylogenetic trees of the detected species were given. This research takes place to be the first study on identifying mussel parasites by using molecular techniques. Also, Mytilicola orientalis is the first record from Turkish coastal waters.