| Summary: | Pseudotsuga brevifolia (Pinaceae) is endemic to limestone habitats in southwest China, and its population size is small and suffers risks of extinction. To detect reasons in explaining the endangered status of P. brevifolia, we here genotyped four natural populations using restriction site-related DNA sequencing (RAD-Seq). The four populations exhibited relatively high genetic diversity (Ho = 0.50–0.52, π = 0.31–0.33). The genetic differentiation between populations was low (FST = 0.028–0.048), with high gene flow (Nm = 4.97–8.66). Analysis of molecular variance showed that the genetic variation was mainly from within individuals (95%). The populations of P. brevifolia declined three times consistent with the Naynayxungla Glaciation (0.8–0.5 Mya), Lushan Glacial Period (∼0.3 Mya) and the Last Interglacial Period (LGP) (10–70 Kya). The results suggested that history cooling events but not genetic factors contributed to the endangered status of P. brevifolia.
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