The results of this first molecular diagnosis and prevalence study of T. equi in horses from Jalisco, Mexico suggest that the parasite is present at sub-clinical levels in western Mexico. Consequently, these horses act as T. equi carriers that can contribute to the spread of EP. Our findings call for the need to study local tick species and to obtain the molecular characterization of existing T. equi strains. Only through conducting a comprehensive EP epidemiologic study that includes different regions in each country will it be possible to implement an appropriate national prevention and control strategy.