A survey of Babesia, Theileria and Hepatozoon was conducted in wild mammals, including the capybara (Hydrochaeris hydrochaeris; n = 14) from Brazil, the jaguar (Panthera onca; n = 2) and crab-eating raccoon (Procyon cancrivorus; n = 4) from Venezuela, and the red deer (Cervus elaphus; n = 70), red squirrel (Sciurus vulgaris; n = 5) and Eurasian pine marten (Martes martes; n = 3) from Spain. Diagnostic procedures included both microscopy and molecular methods (PCR and sequencing of the 18S rRNA gene). Microscopic examination of blood smears revealed no hematozoan infections -unlike the molecular analyses. Nine Brazilian capybaras were found to be infected with Hepatozoon canis (prevalence 64%), two of which were coinfected with a previously unknown babesid (prevalence 14%) loosely related to Theileria equi (90% 18S rRNA gene similarity according to BLASTN ® analysis).One jaguar and one crab-eating raccoon from Venezuela were infected by H. canis. Four of the red deer were infected with theilerids (5.7% prevalence), two with Theileria sp. and two with T. annulata. One red squirrel and three pine martens were infected with Hepatozoon sp. The isolate form the red squirrel was phylogenetically related to Hepatozoon sp. reported in Spanish bank voles, whereas those infecting the pine martens were related to Hepatozoon felis reported in Spanish cats. In conclusion, the molecular findings show that some non-canid mammals are carriers of H. canis in South America, while red deer may carry T. annulata in Europe. Small mammals in Europe appear to be unlikely hosts of H. canis and H. felis.