Each species within the order Thysanoptera has a distinct mitochondrial gene order displaying a high level of gene rearrangement, particularly massive in Phlaeothripidae. To understand the evolutionary patterns of rearrangement in this family, we sequenced the complete mitochondrial genome of Psephenothrips eriobotryae, a notable potential pest of loquat trees. Its mitogenome is a circular DNA molecule (15,413 bp in size) composed of 37 genes: 13 PCGs, 22 tRNAs, two rRNAs, and two putative control regions (CRs). By comparing with the ancestral mitogenome of arthropods, P. eriobotryae exhibits notable gene rearrangement variations. However, it shares four conserved gene blocks with three closely related species in Phlaeothripinae. In the phylogenetic tree, P. eriobotryae was clustered with these three leaf-feeding Phlaeothripinae species. The presence of more similar conserved gene blocks probably indicates a strong correlation between gene rearrangements and the phylogeny within Phlaeothripidae. Furthermore, the mitogenome of P. eriobotryae shows some characteristics: (a) two putative CRs in which CR2 is the copy of partial CR1 with 99.62% sequence similarity, and CR1 consists of two 237 bp repeat unites; (b) high A+T content of 82.6% in overall base composition; (c) trnS1 lacking a complete dihydrouridine (DHU) arm; (d) the protein coding gene, atp8 started with TTG instead of the more common ATN, while nad3 terminated by TAG rather than TAA; (e) translocations and inversions observed in fifteen of the 37 genes.