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Dendrocalamus membranaceus Munro is a woody bamboo with a high economic and ecological value that often occurs as natural stands, such as in the large-scale forested areas of China's Yunnan Province. Due to its overexploitation, the habitat of D. membranaceus in Yunnan has been dramatically reduced, and the quality of the stands has declined. As a preliminary analysis in considering the effective protection for these germplasm resources, we assessed the genetic diversity of 12 natural populations in Yunnan, using inter-simple sequence repeat (ISSR) markers. From 10 ISSR primers, we generated 155 bands, of which 153 were polymorphic (98.71%). Compared with other species in the genus, this species demonstrated a greater genetic diversity (S = 0.349) and lower genetic differentiation (GST = 0.252). Our analysis of molecular variance revealed that the genetic differentiation among the populations is significant. A large proportion of the genetic variation (78.95%) resides among the individuals within populations, whereas only 21.05% are found among populations. Mantel tests indicated no significant correlation between genetic and geographic distances among the populations. Given the low sexual reproducibility and characteristics of monocarpic plants, we recommend implementing in situ conservation measures for all of the D. membranaceus populations in Yunnan and collecting sufficient samples for ex situ conservation. Furthermore, the conservation area should be extended to its main natural habitats, the Lancang-Mekong River Valley. [ABSTRACT FROM AUTHOR]