(Uploaded by Plazi for the Bat Literature Project) The Thomas's horseshoe bat (Rhinolophus thomasi) is restricted to southeast Asia and few studies have been conducted on this species. Here we characterized the complete mitochondrial genome of R. thomasi using next-generation sequencing and Sanger sequencing. The whole mitogenome is 16,899 bp in length and contains 22 tRNA, 2 rRNA, 13 protein-coding genes and a non-coding control region. The tissue used in this study was taken from a sample collected 13 years ago and the genomic DNA was seriously degraded. Our study adds to a growing number of studies indicating that next-generation sequencing is powerful in generating genetic/genomic resources from museum samples.