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Theileria equiand Babesia caballiare tick-borne protozoan parasites that can cause anemia in horses. In the Philippines, serological detection of these parasites has only been reported in the Northern area (Luzon). In this study, 105 horses from Cebu and Bohol, Philippines were tested using peripheral blood smear examination (PBSE), immunochromatographic test (ICT) strips, and PCR. Clinical history, presenting clinical signs and complete blood count were obtained. Results revealed that although all horses were negative using PBSE, 23 (21.9%) were positive (12 for T. equi, and 11 for B. caballi) using ICT. PCR revealed 26 and 2 horses positive for T. equiand B. caballi, respectively. All positive horses showed no clinical signs. Partial DNA sequences of representative amplicons were found 100% identical to GenBank registered T. equiand B. caballisequences. Statistical analyses revealed that location was found associated with T. equiPCR positivity and B. caballiseropositivity. This study documents the first serological detection of T. equiand B. caballiin horses in the southern area of the Philippines, and their first molecular detection and characterization in the country.