Korean fir (Abies koreana) has been cultivated for less than 100 years, mainly in the United States and Europe. Using nuclear microsatellite, mitochondrial, and chloroplast markers, we investigated the origin of cultivated korean fir from South Korea (KC group) as well as the United States and United Kingdom (EU group), and compared these samples to published data from wild populations. All genotypes in the EU and KC groups were most closely related to the wild individuals from Mt. Hallasan, the southernmost A. koreana population on Jejudo Island (South Korea). However, the presence of the chloroplast haplotypes clustered with Abies balsamea in two EU cultivars and the higher diversity values of the EU group compared with the wild individuals from Mt. Hallasan infer a certain level of introgression from different species during cultivation. The EU group had a higher inbreeding coefficient and linkage disequilibrium, and a smaller proportion of rare alleles, than the wild populations. This suggests that the genetic characteristics of korean fir cultivars reflect strong artificial selection pressure for desirable horticultural traits and asexual reproduction. Last, this genetic background study suggests that the other wild populations in the Korean peninsula can serve as valuable genetic resources for future breeding.