The yellow-legged hornet, Vespa velutina nigrithorax (Hymenoptera: Vespidae), invaded into South Korea in 2003. Currently, V. velutina is distributed throughout South Korean regions,. A genetic trait of invasive species provides important data for environmental risk assessment. In this study, we analysed the genetic variation of the V. velutina among the populations of South Korea and other foreign countries using partial sequences of mitochondrial COI, CytB and 16S rRNA. We further developed intergenic spacers (IGS2 and IGS3) to detect genetic variation among Korean populations. Each single haplotype was recovered from the domestic V. velutina from each coding gene sequence. Korean individuals shared the haplotype with that of Japan and China. Phylogenetic analysis (excluding 16S rRNA) using available sequences and ours showed the presence of two groups: the Indonesia and Malaysia group and another group (Korea, Japan, China, France, Vietnam and Thailand). The newly developed IGS2 and IGS3 markers resulted in each seven and four haplotypes, providing better resolution than coding gene sequences. Analysis of Molecular Variance using the combined sequences of IGS2 and IGS3 showed that the majority of variance was allocated to each population and only minority of variance is allocated to among-populations. This result may indicate that the V. v. nigrithorax invaded in Korea shows a single panmictic population and this possibly suggest that Korean population may have originated from small founder individuals.