We have determined the mitochondrial genome of Chilo suppressalis (Walker, 1863) collected in Korea. The circular mitogenome of C. suppressalis was 15,341 bp including 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNAs, and a single large non-coding region of 622 bp. The base composition was AT-biased (95.4\%). Through alignment of three C. suppresalis mitochondrial genomes, 79 single nucleotide polymorphisms (8.8\%) and 291 insertions and deletions (33.3\%) are identified as Korean C. suppressalis specific variations. Phylogenetic trees present that three mitochondrial genomes of C. suppressalis have enough variations within a species, which can be a candidate to understand its origin and geographical distribution using molecular marker sequences.