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Background  Improved knowledge on vector-borne pathogens in wildlife will help determine their effect on host species at the population and individual level and whether these are affected by anthropogenic factors such as global climate change and landscape changes. Here, samples from brown hyenas ( Parahyaena brunnea ) from Namibia (BHNA) and spotted hyenas ( Crocuta crocuta ) 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.    Methods  Tissue samples from BHNA ( n  = 17), SHNA ( n  = 19) and SHTZ ( n  = 25) were analysed by PCRs targeting Anaplasmataceae,  Rickettsia  spp., piroplasms, specifically  Babesia lengau -like piroplasms, Hepatozoidae and filarioids. After sequencing, maximum-likelihood phylogenetic analyses were conducted.    Results  The relative frequency of Anaplasmataceae was significantly higher in BHNA (82.4%) and SHNA (100.0%) than in SHTZ (32.0%). Only  Anaplasma phagocytophilum / platys -like and  Anaplasma bovis -like sequences were detected.  Rickettsia raoultii  was found in one BHNA and three SHTZ. This is the first report of  R. raoultii  from sub-Saharan Africa.  Babesia lengau -like piroplasms were found in 70.6% of BHNA, 88.9% of SHNA and 32.0% of SHTZ, showing higher sequence diversity than  B. lengau  from South African cheetahs ( Acinonyx jubatus ). In one SHTZ, a  Babesia vogeli -like sequence was identified.  Hepatozoon felis -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  H. felis  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 1–4; SHNA median 3 pathogens, range 2–4) and significantly rarer in SHTZ (median 1, range 0–4, 9 individuals uninfected).    Conclusions  The frequencies of all pathogens groups were high, and except for  Rickettsia , multiple species and genotypes were identified for each pathogen group. Ecological conditions explained pathogen identity and diversity better than host taxonomy.    Graphic AbstractSupplementary Information  The online version contains supplementary material available at 10.1186/s13071-021-04835-x.

parasites and vectors

Genetic diversity of vector-borne pathogens in spotted and brown hyenas from Namibia and Tanzania relates to ecological conditions rather than host taxonomy