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Deutzianthus tonkinensis (Euphorbiaceae) is an endangered but commercially popular oil-producing tree, whose populations in China are now fragmented, with the total number of individuals decreasing steadily. Here, we characterized the chloroplast (cp) genome of D. tonkinensis using the genome skimming approach. The whole cp genome is 163,481 bp and comprises 134 genes, including eight unique rRNAs, 36 tRNAs, 84 protein-coding genes, and two pseudo-genes (ycf15 and rps16). The overall guanine-cytosine content of D. tonkinensis cp genome is 35.7%. The phylogenetic analysis suggested that D. tonkinensis is closely related to the Vernicia genus. This study will be useful for future studies on endangered oil-producing tree species, and provide a basis for conservation of this important resource plant.