Gobies and their ectoparasitic monogenean flatworms are promising models for species diversification because of their species richness. Recent decades have seen the discovery of several new species of Gyrodactylus (Monogenea: Gyrodactylidae) on European gobies, mostly in the sand goby lineage and especially in the Eastern Mediterranean. However, the monogenean fauna of other gobies is much less understood. Therefore, we scrutinized five gobiid species (34 specimens, vouchered, with some representatives sequenced), sampled in Greece, for monogenean ectoparasites. Only specimens of the giant goby Gobius cobitis were infected; they harbored Xenoligophoroides cobitis (Monogenea: Dactylogyridae) on their gills. Here we provide the first record from Greece, and the first ITS rDNA and COI sequences of the representative of this monotypic genus. Also 28S rDNA was sequenced and compared with published data from across its known distribution, suggesting clinal variation. Lack of sequence data of closely related dactylogyrid monogeneans prevents either proposing a sister-group for Xenoligophoroides, or inferring a scenario explaining the presence of a single known member of this genus on gobies. Possible hypotheses include either the ancestral long-term presence on gobiids but “missing the boat” of the diversification events in the “Gobius-lineage”, or a recent host switch from a non-gobiid host.