Among vector-borne protozoaHepatozoon felisandCytauxzoon europaeusare considered emerging species in felids in Europe. To investigate the presence of these two protozoa 127 domestic cats and 4 wildcats were screened by PCRs targeting the18SrRNA gene ofHepatozoonspp. and piroplasms, as well as thecytbgene ofCytauxzoonspp. The samples were collected inside and outside a region of Hungary, where both protozoan groups are endemic in wildcats. Among domestic cats, one proved to be infected withH. felis. Furthermore, spleen samples of four wildcats were also examined, among which three tested positive forH. felis, and one had co-infection withC. europaeus. Importantly,H. felisfrom the co-infected wildcat belonged to genogroup II, similarly toH. felisfrom the positive domestic cat. Based on phylogenetic evidence, this genogroup probably represents a separate species from genogroup I ofH. felis, which was hitherto reported from Mediterranean countries in Europe. The two other wildcats also harboredH. felisfrom genogroup I. NeitherHepatozoonnorCytauxzooninfections were detected outside the recently discovered endemic region. In conclusion, this study demonstrates for the first time in Europe thatH. felisfrom genogroup II may emerge in free-roaming domestic cats in regions where this protozoan parasite is endemic in wildcats.