Abstract Background Within the African monitor lizard family Varanidae, two haemogregarine genera have been reported. These comprise five species of Hepatozoon Miller, 1908 and a species of Haemogregarina Danilewsky, 1885. Even though other haemogregarine genera such as Hemolivia Petit, Landau, Baccam & Lainson, 1990 and Karyolysus Labbé, 1894 have been reported parasitising other lizard families, these have not been found infecting the Varanidae. The genus Karyolysus has to date been formally described and named only from lizards of the family Lacertidae and to the authors’ knowledge, this includes only nine species. Molecular characterisation using fragments of the 18S gene has only recently been completed for but two of these species. To date, three Hepatozoon species are known from southern African varanids, one of these Hepatozoon paradoxa (Dias, 1954) shares morphological characteristics alike to species of the family Karyolysidae. Thus, this study aimed to morphologically redescribe and characterise H. paradoxa molecularly, so as to determine its taxonomic placement. Methods Specimens of Varanus albigularis albigularis Daudin, 1802 (Rock monitor) and Varanus niloticus (Linnaeus in Hasselquist, 1762) (Nile monitor) were collected from the Ndumo Game Reserve, South Africa. Upon capture animals were examined for haematophagous arthropods. Blood was collected, thin blood smears prepared, stained with Giemsa, screened and micrographs of parasites captured. Haemogregarine morphometric data were compared with the data for named haemogregarines of African varanids. Primer set HepF300 and HepR900 was employed to target a fragment of the 18S rRNA gene and resulting sequences compared with other known haemogregarine sequences selected from the GenBank database. Results Hepatozoon paradoxa was identified infecting two out of eight (25 %) V. a. albigularis and a single (100 %) V. niloticus examined. Phylogenetic analyses revealed that H. paradoxa clustered with the ‘ Karyolysus ’ clade, and not with those of reptilian Hepatozoon spp. Conclusions In addition to this being the first morphological and molecular characterisation of a haemogregarine within the African Varanidae, it is the first report of a species of Karyolysus infecting the monitor lizard family. Furthermore, this constitutes now only the third described and named Karyolysus species for which there is a nucleotide sequence available.