Equine piroplasmosis (EP) is a tick-borne disease of equids, caused by the two haemoprotozoal parasites: Theileria equi and Babesia caballi. Nigeria constitutes a major crossroads of animal transport in West Africa and may serve as a factor in EP dissemination in the region. The study aim was to characterize EP parasites in donkeys and horses in northern Nigeria using a molecular approach. Blood was collected from 57 donkeys and 47 horses. EP infection was detected and characterized by polymerase chain reaction (PCR). Twenty five donkeys (43.8%) were infected with T. equi, five (8.8%) with B. caballi, three (5.3%) with dual infections. Four horses (8.5%) were infected by T. equi and none by B. caballi. Four of the five known T. equi 18S rRNA genotypes (A, B, C and D) were identified. Theileria equi ema-1 and ema-2 genes were amplified in only 2 and 10 samples, respectively, showing no genetic variation. All B. caballi isolates were classified as rap-1 genotype A1. Twenty-two (42.3%) of the donkeys were positive for anti-T. equi antibodies and 29 (55.8%) were positive for anti-B. caballi antibodies, using immunofluorescence antibody test (IFAT). The study results demonstrate high genetic variation within T. equi parasites, suggesting that donkeys may be reservoirs of EP parasites in West Africa.