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Background The African leopard Panthera pardus pardus (L.) is currently listed as a vulnerable species on the IUCN (International Union for the Conservation of Nature) red list of threatened species due to ongoing population declines. This implies that leopard-specific parasites are also vulnerable to extinction. Intracellular apicomplexan haemoparasites from the genus Hepatozoon Miller, 1908 have been widely reported from wild carnivores in Africa, including non-specific reports from leopards. This paper describes two new haemogregarines in captive and wild leopards from South Africa and provides a tabular summary of these species in relation to species of Hepatozoon reported from mammalian carnivores. Methods Blood was collected from nine captive and eight wild leopards at various localities throughout South Africa. Thin blood smears were Giemsa-stained and screened for intraleukocytic haemoparasites. Gamont stages were micrographed and morphometrically compared with existing literature pertaining to infections in felid hosts. Haemogregarine specific primer set 4558F and 2733R was used to target the 18S rRNA gene for molecular analysis. Resulting sequences were compared to each other and with other available representative mammalian carnivore Hepatozoon sequences from GenBank. Results Two species of Hepatozoon were found in captive and wild leopards. Of the 17 leopards screened, eight were infected with one or both morphologically and genetically distinct haemogregarines. When compared with other species of Hepatozoon reported from felids, the two species from this study were morphometrically and molecularly distinct. Species of Hepatozoon from this study were observed to exclusively parasitize a particular type of leukocyte, with Hepatozoon luiperdjie n. sp. infecting neutrophils and Hepatozoon ingwe n. sp. infecting lymphocytes. Phylogenetic analysis showed that these haemogregarines are genetically distinct, with Hepatozoon luiperdjie n. sp. and Hepatozoon ingwe n. sp. falling in well supported separate clades. Conclusions To our knowledge, this is the first morphometric and molecular description of Hepatozoon in captive and wild African leopards in South Africa. This study highlights the value of using both morphometric and molecular characteristics when describing species of Hepatozoon from felid hosts.