A cross-sectional study was conducted in Submountain undulating, Undulating plain, Western and Western plain agro-climatic zones of Punjab province, India, to determine the prevalence, agreement between diagnostic tests and associated related risk factors of Theileria equi and Babesia caballi infection in equids (horses, donkey, mules). An overall prevalence of 14.14 and 0.0% of T. equi and B. caballi was recorded by multiplex polymerase chain reaction targeting 18S ribosomal RNA (rRNA) for both the parasites and 75 and 1.11% by competitive enzyme-linked immunosorbent assay in a representative sample of 180 animals. Only two animals with positive antibody titre from B. caballi and none with PCR indicated T. equi as the predominant haemoprotozoan responsible for equine piroplasmosis in the study area. Among the PCR-positive animals, presence of tick vectors in farm vicinity was the most influential associated with T. equi infection (P = 0.002; odds ratio (OR) 9.30; 95% confidence interval (CI) = 3.32-27.10). For animals with higher anti-T. equi antibody titres, strong association of sero-prevalence for T. equi was recorded with age, sex, usage, tick infestation and deworming/vaccination status of host animals and farm management strategies. The study has demonstrated the possible absence of B. caballi in both conducive and non-conducive areas of Punjab and demonstrated T. equi as the potential agent of equine piroplasmosis in Punjab.