Branchiobdellidans are ectosymbiotic annelids primarily associated with freshwater crayfish. Previous studies of branchiobdellidans in Croatia have been focussed mainly on the distribution and diversity of the genus Branchiobdella Odier, 1823. The objective of the present research was to infer the phylogenetic relationships of branchiobdellidan species living on crayfish from the genus Austropotamobius Skorikow, 1907 from Croatia and surrounding countries, using mitochondrial cytochrome c oxidase subunit I sequences as a molecular marker. Furthermore, the potential coevolution of branchiobdellidans and their crayfish hosts was examined by comparing the results of the phylogenetic analyses of Branchiobdella and Austropotamobius. The analyses included branchiobdellidans collected from 74 populations of Au. torrentium (Schrank, 1803) and Au. pallipes (Lereboullet, 1858), and established the presence of five branchiobdellidan species: Branchiobdella astaci Odier, 1823, B. hexadonta Grüber, 1883, B. italica Canegallo, 1928, B. parasita (Braun, 1805) and B. pentadonta Whitman, 1882. The results of the phylogenetic analyses were congruent with the results of morphological identification, revealing high diversity of the branchiobdellidan fauna in Croatia. High observed intraspecific p-distance values, in some cases exceeding interspecific distances, imply the existence of cryptic taxa. Furthermore, observed congruent phylogenetic patterns within Austropotamobius and within studied branchiobdellidans indicate similar evolutionary histories, implying their coevolution.