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Knowledge of population genetic structure and intra-population genetic variation is important for understanding population dynamics and evolutionary processes.Dendrobium nobile is a traditional Chinese tonic medicine.In order to analyze the population differentiation and genetic diversity in D.nobile and propose proper conservation measurements, we genotyped 102 individual plants from 7 natural populations distributed across southwest China at 9 microsatellite loci.Seven pairs of primers were newly designed and two pairs were chosen from the EST-SSRs.According to the results, the genetic process of D.nobile on Hainan Island and the Chinese mainland might be affected by different genetic factors.First, the distribution of D.nobile in Hainan Island was highly differentiated and displayed relatively low levels of genetic diversity.Second, only Hainan Island population showed signs of recent population decline (i.e.bottlenecks), and a unidirectional gene flow from the mainland to the Island was detected.The Mantel tests suggested significant positive correlation between the fixation index (Fst) and geographic distance only when Hainan Island was included in the analysis.These results suggested that population bottleneck events might play a more important role in shaping the genetic constitution of the Island population compared with the mainland populations.