The highly valuable timber species Dalbergia cochinchinensis is severely threatened due to habitat loss and illegal logging throughout its distribution in mainland Southeast Asia and is listed on CITES Appendix II. This study proposes a strategy for conservation and sustainable management of the species based on assessment of genetic structure within and among natural populations. We developed SNP markers from RAD sequencing and used these in combination with SSR genotypes from a previous study to analyze the genetic diversity in 26 populations of D. cochinchinensis across its entire range in Laos, Thailand, Cambodia and Vietnam. The species is able of clonal reproduction and we found that trees closer than 45 meters from each other can be clones. Genetic diversity and clustering analysis showed a clear division of populations into five geographical groups with differing levels of diversity. Assignment tests correctly identified the region of origin for approximately 90% of the samples, which demonstrates that despite a low number of successfully developed SNPs, the SSR+SNP marker panel has the potential for tracking the geographic origin of D. cochinchinensis timber for use in CITES regulation and enforcement. We propose the five identified groups to be considered as Management Units and that conservation and breeding programs should be based on a network of in situ and ex situ conservation stands representing the genetic variation among and within these units. We recommend that conservation efforts are directed towards community owned and managed lands, as this has proven an effective strategy locally.