A previous studies depicting origin and sequence variability of the species using DNA barcoding region with the samples collected from Korea showed relatively low sequence variability. Thus, additional markers that reveal higher variability were necessitated to scrutinize population structure in connection with dispersal and invasive dynamics among international populations. Therefore, we sequenced two complete mitochondrial genomes (mitogenomes) of M. pruinosa from the two haplotypes occurring in Korea (H1 and H3). Comparison of the two mitogenomes each with 16,312 and 16,314 bp evidenced that one region located in the A+T-rich region to provide higher number of haplotypes (4 vs. 3), sequence divergence (1.636% vs. 0.636%), and variable sites (7 vs. 3) than those of DNA barcoding region from the screening test using 13 representative individuals. This variable region, in concatenation with the currently available DNA barcoding region might be useful for population genetic analysis of worldwide populations including those of Korea. †These authors contributed equally to this paper.