Wild rodents and their ectoparasites are known reservoirs for various zoonotic pathogens, highlighting the need for detailed studies into their roles in disease transmission. Our research investigated the spatial distribution of rodents and their ectoparasites to better understand the epidemiology of vector‐borne zoonotic diseases (VBZDs), including severe fever with thrombocytopenia syndrome (SFTS), Lyme disease, Q fever, and scrub typhus. We analyzed samples from 540 rodents and 6785 mites, detecting the presence of Borrelia spp., the causative agent of Lyme disease, in 0.9% of rodents and SFTS virus (SFTSV) in 1.0%. In mites, Borrelia spp. and Orientia tsutsugamushi, the bacteria causing scrub typhus, were detected in 0.3% of samples each. Phylogenetic analysis identified the SFTSV sequence as type B3, the Borrelia spp. sequence as B. afzelii, and the O. tsutsugamushi sequence as Karp‐related. Notably, SFTSV was detected for the first time in mites in South Korea, and B. afzelii was found in mites for the first time globally. These findings emphasize the critical need for continuous analysis of VBZDs to anticipate future trends and develop a comprehensive monitoring system. Further research into the rodent and mite populations in South Korea is essential to fully assess the potential risks of VBZDs.