Abstract The complete mitogenomes in order Thysanoptera is limited to subfamily Thripinae heretofore. In the present study, we sequenced the first mitochondrial genome of Neohydatothrips samayunkur (15,295 bp), a member of subfamily Sericothripinae. The genome was characterized by 13 protein-coding genes (PCGs), 22 transfer RNA genes (tRNAs), two ribosomal RNA genes (rRNAs) and three control regions (CRs). This mitogenome had two overlapping regions of 4 bp and twenty four intergenic spacers accounting for 165 bp. All the tRNA had typical cloverleaf secondary structures, except for trnV and trnS which lacked DHU stem and loop. The mitogenomes of N. samayunkur was highly rearranged with many unique features as compared to other thrips mitogenomes, atp6 and nad1 were terminated with TAG and TGA stop codons respectively; location of trnL2 , trnA , trnC , and trnV was rearranged; and the first control region (CR1) was upstream of nad6. The phylogenetic analysis of 13 PCGs implementing maximum likelihood and Bayesian inference showed the clustering of N. samayunkur with Scirtothrips dorsalis supporting the Scirtothrips genus-group and Sericothripinae morphology based relationships. Generation of more mitogenomes from different hierarchical level in the order Thysanoptera is required to understand the gene rearrangements, phylogeny and evolutionary relationships.