Stomoxys and tabanid flies are of medical and veterinary importance because they play crucial roles in disease transmission as mechanical vectors of various hemopathogens. However, its role as a hemoprotozoan parasite vector in horse farms has not been studied. Therefore, we investigated the occurrence of hemoprotozoan parasites belonging to the genera Babesia, Theileria, and Trypanosoma in Stomoxys and tabanid flies using conventional polymerase chain reaction (PCR) and DNA sequencing. All samples (Stomoxys and tabanid flies) were collected using an Nzi trap for three consecutive days each month from November 2022 to March 2023. The flies were morphologically identified to the species level and separated according to sex. Individual (for tabanid flies) or pooled samples (consisting of three specimens of Stomoxys flies of the same species and sex collected from the same site) were used for DNA extraction. Conventional PCR was used to screen for hemoprotozoan parasite DNA, followed by Sanger sequencing to identify the species. In total, 189 biting flies were collected, including four species of Stomoxys (Stomoxys bengalensis, Stomoxys calcitrans, Stomoxys indicus, and Stomoxys sitiens) and five species of tabanids (Atylotus cryptotaxis, Chrysops dispar, Tabanus megalops, Tabanus mesogaeus, and Tabanus rubidus). Stomoxys calcitrans was the most prevalent species, accounting for 58.7% (n = 111) of the collected flies. Ten (12.4%) of the 81 samples (individuals and pools) analyzed by PCR were positive for the 18S rRNA gene of the Theileria/Babesia species. Trypanosoma DNA was not detected in any sample. After performing Basic Local Alignment Search Tool searches and a phylogenetic analysis, only six samples (7.4%), including S. calcitrans (n = 2), S. sitiens (n = 2), T. megalops (n = 1), and A. cryptotaxis (n = 1), were found to be infected with Theileria sinensis. Furthermore, apicomplexan parasites, namely, Mattesia spp. and Colpodella spp., were found on S. indicus, the fungus Meira spp. was found on S. calcitrans, and the pathogenic green alga Helicosporidium spp. was found on A. cryptotaxis. This study is the first to report a variety of Stomoxys and tabanid flies collected from horse farms in Thailand, which were found to be infected with Theileria and Colpodella species that affect mammals, suggesting that Stomoxys and tabanid flies can be used to confirm the presence of hemoprotozoan parasites in the study area. Understanding the presence of hemoprotozoa in flies could help design vector control programs and manage various diseases in the study area.