Introduction: The Theileria annulata is a haemo protozoan parasite that causes economically significant fatal tick-borne diseases in domesticated and wild animals. Methodology: The research focused on identifying Theileria annulata infection in both cattle and buffalo through molecular methods. To achieve this, DNA extraction was conducted using whole blood samples, followed by the design of specific primers for Theileria annulata and subsequent PCR (Polymerase Chain Reaction) analysis. Results: Data were also collected on tick infestation and host-parasite relationship. A total of 2400 Cattle and Buffaloes were evaluated during the study. District-wise detection indicated that the highest rate of infected samples was recorded from Peri-Urban (Cattle=88.33%, Buffalo= 61.94%) and Urban areas (Cattle=65.38%, Buffalo=54.10%) of district Hyderabad, while the lowest rate was recorded from Peri-urban (Cattle=24%, Buffalo=17.9%) and Urban (20.38%, Buffalo=16.66%) areas of district Karachi, Month wise detection of Theileria annulata indicated the highest rate in July (Cattle= 74.0%, Buffalo=47.5%) and the lowest rate in December (Cattle=11.7%, Buffalo=18.1%). The prevalence of parasitic infection showed a notable increase (P<0.05) in the areas of the Suburban region than in Cityscape areas. Conclusion: In the molecular identification of Theileria annulata, the infection rate exhibited a notable difference between District Hyderabad and District Karachi, with a higher prevalence in the former and a lower incidence in the latter. Additionally, cattle displayed greater susceptibility to tick infestation in comparison to buffalo.