Ticks and tick-borne pathogens are one of the major threats to livestock production worldwide. The aim of present study is to specify the molecular epidemiology and its associated risk factors of two well-distributed tick-borne pathogens Anaplasma marginale and Theileria annulata in cattle population from North-western Pakistan. Blood samples were Collected from 60 (32.6 %) local breed cattle, 101 (54.9 %) from crossbreed, and 24 (13.0 %) from exotic breed with total of 184 blood samples. Species-specific PCR assays were performed to detect the presence of A. marginale and T. annulata based on 16S rRNA and 18S rRNA genetic makers respectively. PCR results showed that A. marginale was 16.3 % prevalent and T. annulata was 29.9 % prevalent in the study area with a total prevalence rate of 46.2 % (85/184) of the tested blood samples. District wise analysis revealed that both pathogens were highly prevalent in district Dir Upper (13.6 %) and least prevalent in district Chitral (10.3 %). Univariable analysis of risk factors showed that only breed and acaricidal treatment were significant determinants (P < 0.05) for A. marginale infection, however, in case of T. annulata infection; breed, age, gender, grazing practice, and acaricidal treatment were potential determinants (P < 0.05). Multivariable analysis specified that breed and acaricidal treatment were considered as significant risk factors for A. marginale infection (P < 0.05) whereas acaricidal treatment was found to be a significant determinant for T. annulata infection (P < 0.05). Phylogenetic analysis indicated that A. marginale 16S rRNA and T. annulata 18S rRNA isolates showed similarities and shared phylogeny with same isolates reported from Asia. This is the first molecular report on the epidemiology and risk factors analysis of A. marginale and T. annulata infections in cattle population from NW Pakistan. Further large scale study is required to investigate molecular, epidemiological and genotypic aspects as well as potential risk factors analysis from the c...