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Background  Infections with  Babesia bovis ,  Babesia bigemina, Theileria  species and  Anaplasma marginale  are endemic in Kenya yet there is a lack of adequate information on their genotypes. This study established the genetic diversities of the above tick-borne hemoparasites infecting cattle in Kenya.    Methods  Nested PCR and sequencing were used to determine the prevalence and genetic diversity of the above parasites in 192 cattle blood samples collected from Ngong and Machakos farms.  B. bovis  spherical body protein 4,  B. bigemina  rhoptry-associated protein 1a,  A. marginale  major surface protein 5,  Theileria  spp. 18S rRNA,  T. parva  p104 and  T. orientalis  major piroplasm surface protein were used as the marker genes.    Results   B. bovis ,  B. bigemina ,  T. parva ,  T. velifera ,  T. taurotragi ,  T. mutans  and  A. marginale  were prevalent in both farms, whereas  T. ovis, Theileria  sp .  (buffalo) and  T. orientalis  were found only in Ngong farm. Co-infections were observed in more than 50 % of positive samples in both farms.  Babesia  parasites and  A. marginale  sequences were highly conserved while  T. parva  and  T. orientalis  were polymorphic. Cattle-derived  T. parva  was detected in Machakos farm. However, cattle and buffalo–derived  Theileria  were detected in Ngong farm suggesting interactions between cattle and wild buffaloes. Generally, the pathogens detected in Kenya were genetically related to the other African isolates but different from the isolates in other continents.    Conclusions  The current findings reaffirm the endemicity and co-infection of cattle with tick-borne hemoparasites, and the role of wildlife in pathogens transmission and population genetics in Kenya.    Electronic supplementary material  The online version of this article (doi:10.1186/s13071-015-1106-9) contains supplementary material, which is available to authorized users.

Molecular detection and characterization of Babesia bovis, Babesia bigemina, Theileria species and Anaplasma marginale isolated from cattle in Kenya