This study explores the prevalence, epidemiology, and molecular features of piroplasms in cattle within Azad Jammu and Kashmir (AJK), Pakistan. The investigation utilized both microscopy and Polymerase Chain Reaction (PCR) techniques to screen and analyze 450 blood samples from cattle across different regions of AJK. In addition, we also assessed the correlation between the occurrence of these infections and various epidemiological factors, including age, breed, gender, and seasonality’ after parasitic prevalence. PCR analysis recorded an overall prevalence rate of 9.33% for piroplasms. The specific prevalence of Theileria annulata, Theileria orientalis, Theileria buffeli, Babesia bigemina, and Babesia bovis was found to be 7.5, 0.6, 0.22, 0.22 and 0.44%, respectively. These findings suggest that the prevalence rates of piroplasms in the research area are considerably affected by epidemiological parameters that are trending in that direction. Additionally, the genetic characterization of the piroplasms provided insightful data regarding the strains prevalent in the AJK region and their genetic relations to strains identified globally. This study provides the first comprehensive report to document the molecular prevalence and species co-infection rates of cattle piroplasms in the specified regions. These findings are expected to contribute significantly to the development of effective treatment, control, and prevention strategies, ultimately supporting the enhancement of the local cattle industry.