Sclerodermus harmandi populations were collected from 6 Korean regions (Seoul, Gangwon, Chungcheong, Jeolla, Gyeonasang and Jeju provinces), 1 Chinese region (Nanjing) and 1 Japanese region (Tokyo). Above all was identified as the same species based on morphological characteristics. In present study, we compared the intra-specific characteristics of regional isolated populations of S. harmandi based on nucleotide and amino acid sequences of variant genomic and mitochondrial loci: the full length of internal transcribed spacer 1 and 2 (ITS1 & ITS2), the complete cytochrome oxidase subunit I and II (COI & COII) and tRNA genes for aspartate and lysine and 5'end of ATPase 8 genes. There were no significant differences among the analysed 9 populations regardless of regional segregation. The nucleotide and translated amino acid sequences similarities were significantly high, despite some sequence differences were found in same loci. This result support the report based on the morphological characteristics. However, we are conducting further study to identify whether sequence differences in specific loci are the characteristics of individual level in population or population level and to analyse the full sequences of mitochondrial DNA by regional segregation.