A total of 286 larval forms of Hysterothylacium aduncum were collected from Merlangius merlangus euxinus and Trachurus trachurus captured at different sites of the Black Sea coast of Turkey. Prevalence of H. aduncum in M. merlangus euxinus and T. trachurus was 37.4 and 29.3 %, respectively. The fourth-stage larvae from M. merlangus euxinus and T. trachurus of H. aduncum were characterized genetically using a molecular approach. The ribosomal DNA (rDNA) internal transcribed spacer (ITS) region (ITS-1, 5.8S subunit, ITS-2) was amplified and sequenced. Two isolates of H. aduncum obtained from M. merlangus euxinus and T. trachurus in Black Sea showed a 100 % nucleotide similarity. Pairwise comparison between the entire ITS fragment including ITS-1, 5.8S, ITS-2 sequences of the H. adumcum isolates of M. merlangus euxinus and T. trachurus from Black Sea (Turkey, JX413596-JX413597) and other H. adumcum isolates from Baltic Sea (Poland, AJ937672), North Sea (Denmark, HM598666), Mediterranean Sea (Tunisia, HQ270427), Japan Sea (Japan, AB277826), Adriatic Sea (Croatia, JQ934878), East Greenland Sea, English Channel, Bay of Biscay, Adriatic Sea, and North Sea showed differences ranging from 0.1 to 0.7 %. With the present study, larvae of H. aduncum infecting M. merlangus euxinus and T. trachurus caught off the Black Sea, Turkey were characterized for the first time by sequencing of the ITS rDNA.