The two stork species that nest in Central Europe, Ciconia ciconia and Ciconia nigra, have been repeatedly shown to host the digenetic trematode Cathaemasia hians (Rudolphi, 1809) in their esophagus and muscular stomach. These host species differ in their habitat and food preferences, and the morphologic characters of C. hians isolates ex Ci. nigra and Ci. ciconia are not identical. These differences led to a previous proposal of two subspecies, Cathaemasia hians longivitellata Macko, 1960, and Cathaemasia hians hians Macko, 1960. We hypothesize that the Cathaemasia hians isolates ex Ci. nigra and Ci. ciconia represent two independent species. Therefore, in the present study, we performed the first molecular analyses of C. hians individuals that were consistent with the diagnosis of C. hians hians (ex Ci. nigra) and C. hians longivitellata (ex Ci. ciconia). The combined molecular and comparative morphological analyses of the central European Cathaemasia individuals ex Ci. nigra and Ci. ciconia led to the proposal of a split of C. hians into C. hians sensu stricto (formerly C. hians hians) and C. longivitellata sp. n. (formerly C. hians longivitellata). Morphological analyses confirmed that the length of the vitellaria is the key identification feature of the two previously mentioned species. Both Cathaemasia spp. substantially differ at the molecular level and have strict host specificity, which might be related to differences in the habitat and food preferences of the two stork species.