Triaenophora shennongjiaensis (Orobanchaceae, Lamiales) is a medical herb whose population size in China is extremely small. Thus, there is an urgent need to develop conservation and management strategies for this endangered species. In this study, we determined the complete chloroplast genome of T. shennongjiaensis using Illumina paired-end sequencing data. The plastome is 153 799 bp in length, with a pair of inverted repeat (IR) regions (25 838 bp), one large single copy region (84 649 bp), and one small single copy region (17 474 bp). The plastome contains 133 genes, including 88 protein-coding genes, eight ribosomal RNA genes and 37 transfer RNA genes, 17 of which are duplicated within the IRs. Evolutionary analysis showed that the ndhK gene had potentially undergone positive selection. Phylogenetic analysis based on 20 plastomes of Lamiales indicate that T. shennongjiaensis is closely related to Rehmannia species. Our work contributes to the study of the evolutionary history of Lamiales and conservation management of T. shennongjiaensis.