The rising prevalence of tick borne parasites and their economic impact on livestock production have often demanded better diagnostic tools and timely treatment options. The paper reports the molecular evidence of natural infections of Theileria ovis, T. lestoquardi and T. luwenshuni among goats in Kerala, south India, using PCR and RFLP. Concurrent infection of T. ovis and T. luwenshuni was also identified. Out of 150 samples studied, the PCR protocol was also found to detect a higher prevalence (59.3%) of theileriosis when compared to the detection of piroplasms (30%) in stained blood smears. In this study, the majority of goats were infected with T. ovis (75.28%), followed by those with T. luwenshuni (32.58%) and T. lestoquardi (7.86%). A high proportion of infected goats did not show any clinical signs indicating carrier status of infection. The carrier status of animals also signals the possible risk of disease transmission to healthy stock. However, a high incidence of caprine theileriosis, with significant haematological alterations including macrocytic hypochromic anaemia and thrombocytopenia, poses a potential threat to the goat population in the event of stress. Routine monitoring should be employed in farms for early detection and treatment of carrier animals.