Camel production in Pakistan is adversely affected by several pathogenic infections and insufficient veterinary facilities. Haemoparasitic diseases significantly affect health and productivity of camels causing a substantial financial burden to camel breeders and owners. The present study was designed for the identification and molecular detection of haemoparasites particularly piroplasms (Theileria spp. / Babesia spp.) infection in naturally infected local one-humped camels (Camelus dromedaries) in Punjab by using parasitological as well as molecular tools like polymerase chain reaction (PCR) followed by phylogenetic analysis. Blood samples (n=400) were collected from camels suspected for piroplasms infections in ten districts of Punjab and processed for blood smears and PCR targeting 18S rRNA gene. The findings revealed that Theileria is the most common parasite in camels of all study areas with overall prevalence of 12% and 13.5% by microscopic examination of GSBS and PCR, respectively. The phylogenetic analyses of the isolates on sequencing revealed that all analyzed isolates were closely related to Theileria annulata present in NCBI from several parts of the world. However, all samples tested for presence of Babesia spp. were found negative by microscopy and PCR. Chi square based risk factors analyses exhibited significant (P < 0.05) association between gender, age, tick infestation, previous tick history and prevalence of Theileria. In conclusion, current study on haemoparasites is evident for first ever molecular identification of Theileria annulata infection in camels of Pakistan along with assessment of potential risk factors associated with disease. Recent outcomes are ascertaining it as a silent killer with damaging effects on immune system.