Candidatus Neoehrlichia mikurensis (Ca. N. mikurensis; family Anaplasmataceae) is an emerging tick-borne pathogen that causes a systemic inflammatory syndrome with thrombotic complications. We report here the first identification of Ca. N. mikurensis in organ samples from small mammals captured in southwest South Korea. Nested PCR of groEL and 16S rRNA genes was used to confirm the identity of the bacteria present, and successfully amplified fragments were sequenced. All captured animals were identified as striped field mice (Apodemus agrarius), approximately 28.6% (4/14) and 21.4% (3/14) of which were found to be PCR-positive for Ca. N. mikurensis and Anaplasma phagocytophilum, respectively. The detection of Ca. N. mikurensis in these animals represents the first evidence of this pathogen in South Korea. Carriage of this bacterium by rodents highlights the need for more detailed investigation of their role in its transmission to humans.