Trypanosoma (Megatrypanum) theileri is a non-pathogenic or weakly pathogenic parasite of domestic cattle that is cyclically transmitted by blood-sucking insects, mainly tabanid flies. It has been reported in several countries like Brazil, Venezuela, Japan, Taiwan, Thailand, Vietnam, and the Philippines. Although the ruminant industry is actively expanded in Malaysia, T. theileri and T. theileri-like trypanosomes have never been reported from Malaysia. The low pathogenicity of this species might be the main reason for overlooking T. theileri in this country. This paper describes an unforeseen finding of T. theileri from the outbreak of T. evansi in the state of Kelantan, Malaysia. This is the first time T. theileri reported in Malaysia, and also the first time T. theileri is reported in equid. Clinical signs compatible with infection by blood protozoa were observed; however, it was uncertain whether they were due to T. theileri infection. The detection of T. theileri from the blood sample and Tabanus sp. were confirmed through molecular analysis with PCR and DNA sequencing. In the present study, T. theileri from one horse and one Tabanus sp. were clustered with sequences of the previously described phylogenetic lineages from Japan, Chad and Brazil cattle. Even though this species is claimed to be host-specific with ruminant host restriction, the finding from this study suggested that T. theileri can infect equine whilst other isolates are known to infect ruminant species only. It is suspected there were two genotypes of T. theileri circulating in at least two districts of Kelantan. Thus, further study on multiple DNA regions should be conducted to determine the strains of detected T. theileri in Malaysia. Its impact on the horse and cattle industry should also be revised.