Feline hepatozoonosis is an emerging disease of domestic and wild felids though there is limited knowledge of this infection, e.g. regarding geographical distribution and parasite species involved. The present study evaluated microscopically and molecularly the occurrence of Hepatozoon spp. in domestic cats from insular (Crete, Mykonos and Skopelos) and continental (prefectures of Attica and Thessaloniki) Greece. Out of 282 cats examined, 72 (25.5 %) scored positive by PCR for Hepatozoon spp. and of them, 9 (12.5 %) showed gamonts on the blood smear microscopic examination. Sequences obtained from 35 of the amplicons proved the presence of two haplotypes of Hepatozoon felis. One, herein called H1 (34/35 amplicons) resulted 100 % identical with H. felis from Italy and isolates from other continents, and ∼98 % similar with a H. felis isolate causing severe clinical signs in Austria. The haplotype H2, found in a cat in Skopelos, had ∼94 % identity with H1, with H. felis isolates from Italy, Israel, Spain, a ∼92 % identity with the isolate from Austria, and ∼94−98 % with isolates from South Africa. These are the first records of H. felis in cat populations from Greece and indicate that the infection may be present at high prevalences in different regions of the country. Furthermore, the results of the molecular and phylogenetic analysis support a recent hypothesis indicating the existence of a species-complex classification for H. felis. Further studies aiming at elucidating the genetic make-up of Hepatozoon populations and possible variations in terms of geographic distribution and clinical relevance are necessary. The importance of a continuous epizootiological monitoring is crucial for the establishment of preventative and control measures protecting the health of cats living in or travelling to enzootic areas.