Background Mycterothrips gongshanensis, as a new tea pest, has spread wildly in Guizhou and Yunnan Province, China, and the damage can be comparable to that of the major tea pest Dendrothrips minowai. Though its bionomics have been documented, but lack molecular biology researches. The present study, complete mitochondrial genome of M. gongshanensis was firstly obtained and analysed. Methods and Results We assembled the complete 15,154 bp circular mitochondrial genome of M. gongshanensis by the first-generation sequencing, which included 13 protein-coding genes (PCGs), 22 common tRNA genes, two repetitive tRNA genes (tRNA-Asn, and tRNA-Ile), two rRNA genes, and two control regions. The nucleotide composition is AT-biased (5.20%), with the respectively proportion as follow, 40.64% A, 12.67% C, 10.06% G and 36.62% T. The PCGs, with a whole length of 10,985 bp, the majority were initiated at typical start codons ATN (N, any nucleotide) and terminated with the typical stop codons TAA or TAG, except for atp8 using GTG and single T as start and stop codon, respectively. Additionally, the phylogenetic analysis indicated that M. gongshanensis was a sister group relationship with the genus Thrips, and the tribes Sericothripini and Dendrothripini were recovered as monophyletic group.Conclusions Gene rearrangement consists in the mitochondrial genome of M. gongshanensis, which is most closely related to the Thrips. The results will contribute to the classification and rapid identifucations of Thripidae.