In this study, we have determined mitochondrial genome of Matsucoccus thunbergianae isolated in Korea. The circular mitogenome of M. thunbergianae is 15,406 bp including 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNAs. AT ratio is 78.2\%. Maximum-likelihood and Bayesian inference phylogenetic trees show that M. thunbergianae is clustered with M. matsumurae, and family Margarodidae is clustered with family Pseudococcidae with enough supportive values.