Spodoptera litura Fabricius, 1775 (Lepidoptera: Noctuidae) is a serious crop pest with a long-distance migratory flight. To date, the DNA barcode region has been widely used in genetic diversity analysis studies of Spodoptera litura. However, the DNA barcode region showed maximum variation rate of S. litura, which from 18 regions in South Korea, was 0.608% (nine haplotypes) in previous study. In this study, four mitochondrial genes (ND4, ND4L, ND1, 16s rRNA) have higher intra-specific variation rates than the DNA barcode region. Among the four genes, The variation rate of the 16s rRNA region was confirmed to be a minimum of 0.203% (2bp) and a maximum of 1.824% (18bp). Finally, the 16s rRNA region with the highest PCR amplification efficiency and highest variation rate was selected as a high-efficiency molecular marker.