Severe fever with thrombocytopenia syndrome (SFTS) is an emerging zoonotic tick-borne disease caused by SFTS virus, which circulates among ticks and their host animals, including wildlife. However, few studies have examined SFTS virus infection in wildlife present in the Republic of Korea (ROK). We evaluated SFTS virus infection in tissue samples from Korean water deer (Hydropotes inermis argyropus), one of the most common wild ungulates in ROK. In this study, we evaluated tissue samples of 129 water deer carcasses collected in 2017 and detected SFTS viral RNA by conventional PCR. SFTS viral RNA was found in 3 of the 129 carcasses, showing a prevalence of 2.3 %; 2 of which were collected in Gyeongsangnam-do and 1 of which was in the Gangwon-do region. Among the 6 internal organs studied, only the spleen samples were positive. Phylogenetic analysis revealed close relationships between deer- and human-derived strains. The medium segments of the three positive cases clustered with genotype B, which is the predominant genotype in ROK. In the small segment, two cases clustered with genotype B, samples 17WD044 and 17WD065. The third sample, 17WD068 from Gangwon-do province, showed genotype A, which circulates mainly in China. The disagreement in the genotypes of the two tested segments suggests a potential reassortment between genotype A and B, resulting in genetic recombination as observed in sample 17WD068, which may be co-circulating in China and Korea. Further studies in wildlife and humans are necessary to understand the genetic characteristics of SFTS viruses circulating in ROK.