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Here, samples from brown hyenas (<jats:italic>Parahyaena brunnea<\/jats:italic>) from Namibia (BHNA) and spotted hyenas (<jats:italic>Crocuta crocuta<\/jats:italic>) from Namibia (SHNA) and Tanzania (SHTZ) were screened for vector-borne pathogens to assess the frequency and genetic diversity of pathogens and the effect of ecological conditions and host taxonomy on this diversity.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>Tissue samples from BHNA (<jats:italic>n<\/jats:italic>\u2009=\u200917), SHNA (<jats:italic>n<\/jats:italic>\u2009=\u200919) and SHTZ (<jats:italic>n<\/jats:italic>\u2009=\u200925) were analysed by PCRs targeting Anaplasmataceae, <jats:italic>Rickettsia<\/jats:italic> spp., piroplasms, specifically <jats:italic>Babesia lengau<\/jats:italic>-like piroplasms, Hepatozoidae and filarioids. After sequencing, maximum-likelihood phylogenetic analyses were conducted.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>The relative frequency of Anaplasmataceae was significantly higher in BHNA (82.4%) and SHNA (100.0%) than in SHTZ (32.0%). Only <jats:italic>Anaplasma phagocytophilum<\/jats:italic>\/<jats:italic>platys<\/jats:italic>-like and <jats:italic>Anaplasma bovis<\/jats:italic>-like sequences were detected. <jats:italic>Rickettsia raoultii<\/jats:italic> was found in one BHNA and three SHTZ. This is the first report of <jats:italic>R. raoultii<\/jats:italic> from sub-Saharan Africa. <jats:italic>Babesia lengau<\/jats:italic>-like piroplasms were found in 70.6% of BHNA, 88.9% of SHNA and 32.0% of SHTZ, showing higher sequence diversity than <jats:italic>B. lengau<\/jats:italic> from South African cheetahs (<jats:italic>Acinonyx jubatus<\/jats:italic>). In one SHTZ, a <jats:italic>Babesia vogeli<\/jats:italic>-like sequence was identified. <jats:italic>Hepatozoon felis<\/jats:italic>-like parasites were identified in 64.7% of BHNA, 36.8% of SHNA and 44.0% of SHTZ. Phylogenetic analysis placed the sequences outside the major <jats:italic>H. felis<\/jats:italic> cluster originating from wild and domestic felids. Filarioids were detected in 47.1% of BHNA, 47.4% of SHNA and 36.0% of SHTZ. Phylogenetic analysis revealed high genetic diversity and suggested the presence of several undescribed species. Co-infections were frequently detected in SHNA and BHNA (BHNA median 3 pathogens, range 1\u20134; SHNA median 3 pathogens, range 2\u20134) and significantly rarer in SHTZ (median 1, range 0\u20134, 9 individuals uninfected).<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>The frequencies of all pathogens groups were high, and except for <jats:italic>Rickettsia<\/jats:italic>, multiple species and genotypes were identified for each pathogen group. Ecological conditions explained pathogen identity and diversity better than host taxonomy.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Graphical Abstract<\/jats:title>\n                \n              <\/jats:sec>","DOI":"10.1186\/s13071-021-04835-x","type":"journal-article","created":{"date-parts":[[2021,6,16]],"date-time":"2021-06-16T10:03:22Z","timestamp":1623837802000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Genetic diversity of vector-borne pathogens in spotted and brown hyenas from Namibia and Tanzania relates to ecological conditions rather than host taxonomy"],"prefix":"10.1186","volume":"14","author":[{"given":"J\u00fcrgen","family":"Kr\u00fccken","sequence":"first","affiliation":[]},{"given":"G\u00e1bor \u00c1.","family":"Czirj\u00e1k","sequence":"additional","affiliation":[]},{"given":"Sabrina","family":"Ram\u00fcnke","sequence":"additional","affiliation":[]},{"given":"Maria","family":"Serocki","sequence":"additional","affiliation":[]},{"given":"Sonja K.","family":"Heinrich","sequence":"additional","affiliation":[]},{"given":"J\u00f6rg","family":"Melzheimer","sequence":"additional","affiliation":[]},{"given":"M. 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All experimental procedures, including animal immobilisation and sample collection, were approved by the Internal Ethics Committee of the Leibniz Institute for Zoo and Wildlife Research (Leibniz-IZW, permit number 2002-04-01) and authorised by the Ministry of Environment and Tourism of Namibia (permit numbers 1689\/2012, 1813\/2013 and 1914\/2014) and by the Tanzania Commission for Science and Technology (permit number 2019-146-NA-90-130). All experiments were carried out in compliance with the approved guidelines of the Leibniz-IZW and the laws of Germany, Tanzania and Namibia.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"328"}}