Tick-borne apicomplexan haemoparasites infect wild and domestic animals, but studies on their distribution among free-living animals are comparatively fewer. Tissues from 241 wild carnivores of eight Mustelidae, two Canidae, one Viverridae and one Felidae species were collected in Northern Spain, and analysed by real-time PCR targeting the 18S rRNA gene and sequencing. Babesia vulpes (formerly known as Theileria annae) was the only piroplasm detected in red foxes (Vulpes vulpes). Badgers (Meles meles) were shown to harbour two novel Babesia sp. sequence types (A and B) that only shared 96.7% homology between them and were closely related (ca. 97–98%) to, but distinct from B. vulpes and other babesia from carnivores. Analysis of PCR-derived sequences also revealed the presence of Cystoisospora sp. and Hepatozoon sp. in badgers and showed that wild cats (Felis silvestris catus) were infected with Cytauxzoon sp. Forty-two per cent of the animals subjected to a detailed external examination were parasitized by ixodid ticks, being Ixodes hexagonus and Ixodes ricinus the most abundant species. This study provided novel data on the different haemoparasites that can infect European wild carnivores and showed that they can be hosts for a range of haemoparasites and pose a potential risk for transmission to domestic animals.