Bretschneidera sinensis, a class-I protected wild plant in China, is a relic of the ancient Tertiary tropical flora endemic to Asia. However, little is known about its genetics and phylogeography. To elucidate the current phylogeographic patterns and infer the historical population dynamics of B. sinensis, and to make recommendations for its conservation, three non-coding regions of chloroplast DNA (trnQ-rps16, rps8-rps11, and trnT-trnL) were amplified and sequenced across 256 individuals from 23 populations of B. sinensis, spanning 10 provinces of China. We recognized 13 haplotypes, demonstrating relatively high total haplotype diversity (hT = 0.739). Almost all of the variation existed among populations (98.09%, P < 0.001), but that within populations was low (1.91%, P < 0.001). Strong genetic differentiation was detected among populations (GST = 0.855, P < 0.001) with limited estimations of seed flow (Nm = 0.09), indicating that populations were strongly isolated from one another. According to SAMOVA analysis, populations of B. sinensis in China could be divided into five geographic groups: (1) eastern Yunnan to western Guangxi; (2) Guizhou-Hunan-Hubei; (3) central Guangdong; (4) northwestern Guangdong; and (5) the Luoxiao-Nanling-Wuyi -Yangming Mountain. Network analysis showed that the most ancestral haplotypes were located in the first group, i.e., the eastern Yungui Plateau and in eastern Yunnan, which is regarded as a putative glacial refugia for B. sinensis in China. B. sinensis may have expanded its range eastward from these refugia and experienced bottleneck or founder effects in southeastern China. Populations in Liping (Guizhou Province), Longsheng (Guangxi Province), Huizhou (Guangdong Province), Chongyi (Jiangxi Province), Dong-an (Hunan Province), Pingbian (Yunnan Province) and Xinning (Hunan Province) are proposed as the priority protection units.