Here we determined the mitochondrial genome sequence of a notorious pest, the diamondback moth Plutella xylostella (Lepidoptera: Yponomeutoidea: Plutellidae). The mitochondrial genome contains 37 typical animal mitochondrial genes and an A+T-rich region. The gene arrangement is identical to that of other ditrysian lepidopteran mitochondrial genomes, but different from the ancestral gene arrangement in the non-ditrysian Hepialidae of Lepidoptera. The start codon of the cox1 gene is CGA, which is dissimilar to its homologs in most other insects. In Lepidoptera, cox1 and cox2 have low nucleotide diversities, while the nad6, nad2, and nad3 genes are highly variable. Phylogenetic analyses uncovered the reciprocal monophyly of Ditrysia, Apoditrysia, Obtectomera, and Macrolepidoptera, and the placement of the Hesperiidae within Papilionoidea. Our analyses suggest that the complete mitochondrial genome sequences are a promising marker toward fully resolving the phylogenetic relationships within Lepidoptera.