Gyrodactylus ostendicus n. sp. was exclusively found on fins of the common goby Pomatoschistus microps (Krøyer). The haptoral hard parts are among the smallest described for species of Gyrodactylus. A presumed similarity between the new species and G. harengi Malmberg, 1957 (subgenus Metanephrotus Malmberg, 1964) encouraged a comparative approach. A morphological analysis showed the marginal hook sickles of G. ostendicus to be of quite a different type and similar to those of G. arcuatus Bychowsky sensu Bychowsky & Poljansky (1953) (subgenus Mesonephrotus Malmberg, 1964). The new species has a pharynx with short pharyngeal processes. Its protonephridial system has small bladders, indicating an association with the subgenera Mesonephrotus or Metanephrotus. Molecular phylogenetic analyses, including all of the species of Mesonephrotus and Metanephrotus currently available on the GenBank database, suggested that the new species belongs to Mesonephrotus. Combined morphological and molecular studies of the new species show that G. ostendicus is more closely related to G. arcuatus than to G. harengi.