Abstract: 【Objective】 To clarify the mitochondrial genome structure of Selenothrips rubrocinctus and analyze its phylogenetic relationship based on mitochondrial genome sequence, which could provide molecular evidence for identification and phylogeny of Selenothrips insects. 【Method】 The mitochondrial genome of Selenothrips rubrocinctus was sequenced by using Illumina next-generation sequencing, then assembled and annotated. Maximum likelihood（ML） and Bayesian inference（BI） methods were used to construct the phylogenetic tree of 18 Thripidae species and 1 Phlaeothripidae species based on the sequences of 13 protein-coding genes（PCGs） of mitochondrial genomes, to analyze the phylogenetic relationship between S. rubrocinctus and other thrips. 【Result】 The mitochondrial genome of Selenothrips rubrocinctus was 14984 bp in length, including 37 genes（13 PCGs, 22 tRNA genes, 2 rRNA genes） and 1 non-coding region.There were 19 intergenic regions, and the longest intergenic region was 25 bp. There were 10 gene overlapping regions,and the longest overlapping region was 23 bp.The genome had the typical gene composition and order of mitochondrial genome from most Thysanoptera insects, and the AT content was 72.9%, showing obvious AT bias. Among the 13 PCGs,all genes used ATN as the start codon, except for cox1 used TTG as the start codon; and except for nad6 had TAG as the stop codon, 2 genes（nad2 and cox2） had incomplete T as the stop codon, another 10 used TAA as the stop codon.Among the 22 tRNA genes, the 17 tRNA genes could form the complete clover-leaf secondary structures, except trnR,trnS2, and trnY lacked TΨC ring, trnS1 and trnV lacked DHU ring. Phylogenetic analysis showed that Selenothrips rubrocinctus clustered on the same small branch with Rhipiphorothrips cruentatus, and they were closely related.【Conclusion】 The mitochondrial genome structure, composition and gene sequence of Selenothrips rubrocinctus are conserved, consistent with that of other species of Thripidea. Panchaetothripinae is monophyletic and Selenothrips rubrocinctus is closely related to Rhipiphorothrips cruentatus.