Abstract: The research aims at analyzing genetic relationship between wild and domesticated Bletilla striata populations in different areas, and providing support for the protection and utilization of B. striata resources. With RAPD and ISSR markers, at the molecular level, the study identified the differences of genetic diversity among 12 B. striata resources in Hunan, Hubei, Guizhou, Yunnan and Jiangxi. The cluster analysis was used to analyze the differences by UPGMA. The results showed that in 36 RAPD primers, 13 primers got clear band and high polymorphism. In 15 ISSR primers, 2 primers obtained clear band with high polymorphism, and 40 polymorphic bands. UPGMA cluster analysis showed that high genetic diversity was found among 12 B. striata resources. The genetic distance reached up to 0.975. The selected materials were divided into two branches: Hunan, Jiangxi as a branch, Hubei, Guizhou and Yunnan as another branch. RAPD and ISSR markers could reveal the genetic diversity of B. striata resources at the molecular level. Besides, it was found that ISSR markers could amplify more polymorphic bands and get higher polymorphic ratio than that of RAPD markers. And the conducting analysis was not restricted by time and place, and the analysis results were also more stable and reliable. It was concluded that there were some correlations between the differences of genetic diversity among the B. striata populations and geographic locations, which provided related data and theory to further study on B. striata species evolution and genetic diversity.