The purpose of this study was to investigate molecular epidemiology of Theileria spp. in ticks in Korea and assess their potential threat from wildlife animals to domestic animals. A total of 21152 hard ticks were collected from Chungcheong and Jeolla provinces of Korea from March to October 2021. Tick species were identified by microscopy and Theileria spp. were screened by nested PCR targeting 18S rRNA. Haemaphysalis spp. were the most abundant tick species, followed by H. longicornis, H. flava, Amblyomma testudinarium, and Ixodes nipponensis. Of the collected ticks, 6914 ticks (541 pools) were screened, and PCR showed 211 positive pools (39.0%; MIR: 3.05). The PCR and phylogenetic analysis identified two Theileria species, T. luwenshuni and Theileria sp., with T. luwenshuni (162/211, 76.78%; MIR: 2.34) being more abundant than Theileria sp. (36/211, 17.06%; MIR: 0.52); co-infection of the two species were noted (13/211, 6.16%; MIR: 0.19). Among the tick species, H. longicornis, especially nymphs, showed the highest prevalence. Regarding season, the highest prevalence was observed in May. Considering the tick and Theileria species identified in this study, H. longicornis nymph and cervine play a critical role in maintaining Theileria spp. in Korea and could be a potential threat to domestic animals, including deer and goats. In addition, there are significant correlations among tick distribution, region, season, and prevalence of Theileria.