We present here the whole-genome sequence of a thermophilic chemolithotrophic sulfate-reducing bacterium, Thermodesulfomicrobium sp. strain WS (class Deltaproteobacteria), isolated from Onikobe geothermal field (Miyagi Prefecture, Japan). The genome consists of a 2,357,780-bp chromosome with a 62.9% GC content and 2,196 protein-coding sequences.