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Among vector-borne protozoa <i>Hepatozoon felis</i> and <i>Cytauxzoon europaeus</i> are 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 the <i>18S</i> rRNA gene of <i>Hepatozoon</i> spp. and piroplasms, as well as the <i>cytb</i> gene of <i>Cytauxzoon</i> spp. 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 with <i>H. felis</i>. Furthermore, spleen samples of four wildcats were also examined, among which three tested positive for <i>H. felis</i>, and one had co-infection with <i>C. europaeus</i>. Importantly, <i>H. felis</i> from the co-infected wildcat belonged to genogroup II, similarly to <i>H. felis</i> from the positive domestic cat. Based on phylogenetic evidence, this genogroup probably represents a separate species from genogroup I of <i>H. felis</i>, which was hitherto reported from Mediterranean countries in Europe. The two other wildcats also harbored <i>H. felis</i> from genogroup I. Neither <i>Hepatozoon</i> nor <i>Cytauxzoon</i> infections were detected outside the recently discovered endemic region. In conclusion, this study demonstrates for the first time in Europe that <i>H. felis</i> from genogroup II may emerge in free-roaming domestic cats in regions where this protozoan parasite is endemic in wildcats.