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.

Ardisia crenata Sims, one of the most widely distributed Ardisia in the world, is an important ornamental and medicinal plant species. Using seven polymorphic nuclear microsatellite loci, we studied the genetic variation of 20 natural populations of A. crenata across its distribution center in south China. Significant deviation from the Hardy–Weinberg equilibrium in all populations and at all loci were detected, and the fixation index was high (FIS= 0.725), indicating that inbreeding may be dominant in the mixed mating system of this self‐compatible species. The average genetic diversity within populations was relatively low (HS= 0.321). There was significant genetic differentiation among populations (FST= 0.583), which may have resulted from a high level of inbreeding and a low level of gene flow. Ardisia crenata in south China can be roughly divided into an eastern group and a western group, consistent with the floristic division of the Sino‐Himalayan forest subkingdom and the Sino‐Japanese forest subkingdom. There may be separated glacial refugia in each region.

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