Piroplasm parasites of the genera Babesia and Theileria are widely distributed in wildlife and are maintained through complex host–vector transmission systems. Rodents play important roles as reservoir hosts for various arthropod-borne pathogens; however, comparative investigations integrating multiple host compartments and host-associated ectoparasites remain limited. In this study, we conducted a nationwide molecular survey of Babesia and Theileria species in wild rodents and mites collected from rodents in Korea. Rodent blood and liver tissues, together with mite pools, were examined using PCR-based detection methods, and spatial and seasonal variation in pathogen detection patterns was evaluated. Babesia microti was detected in both rodent blood and liver tissues, with higher positivity in blood and marked spatial and seasonal heterogeneity. The higher positivity observed in blood was consistent with the intraerythrocytic biology of B. microti, although differences in analytical sensitivity between sample types were not evaluated. Theileria capreoli DNA was detected exclusively at low frequency in mite pools, whereas Theileria luwenshuni DNA was detected at low frequency in both rodents and mite pools. Because mites are not established biological vectors of these Theileria species, detections in mite pools were interpreted as molecular occurrence rather than evidence of transmission or vector competence. Significant regional and seasonal variation was observed in blood and mite samples; however, overall detection frequencies were low, warranting cautious ecological interpretation. This nationwide, multi-compartment assessment highlights the ecological complexity of piroplasm circulation in wildlife systems and underscores the importance of integrated surveillance approaches when interpreting parasite DNA detection in arthropod assemblages.