This study performed molecular detection and analysis of the heterogeneity of the 18S rRNA gene isolates obtained from equids such as horse, mule, donkey and pony from Erbil province, Kurdistan region of Iraq. Multiplex polymerase chain reaction (PCR) indicated that 76/136 (55.88%) of equine were infected with piroplasms, with Theileria equi (P=41.91%; CI=3.76-14.77%) more prevalent than Babesia caballi (P=8.82%; CI=1.00%), while mixed infection was less (P=5.15%; CI=0.21-1.46%) with a significant difference (P<0.001). There was a significant association between the prevalence of T. equi and recreation (p<0.03) or racing (p<0.02), and but neither the type of equids nor the gender and age groups was significantly associated with prevalence. The obtained sequences were utilized for characterizing the genotypes and phylogeny of both the protozoa. BLAST analysis indicated 98-100% similarity to species isolated in Turkey, Malaysia, Egypt, Sudan, Jordan, Iran, Brazil and South Africa. Four 18S rRNA genotype clades were observed for T. equi (A, B, C and D) and two for B. caballi (A and B). Genetic variation found among the equids in Erbil province is probably due to introduction of equines from other countries without quarantine measures. This study indicates that infection with T. equi is more prevalent than that of B. caballi in the studied area.