Epipactis flava Seidenf. is the only rheophytic orchid found in Thailand. Specific habitat requirements and environmental changes of the growing area have now resulted in E. flava becoming an endangered species and appropriate management protocol is essential. Genetic diversity and population structure of E. flava were evaluated using RAPD and SRAP markers. Nine RAPD primers were selected with 95.93% polymorphism and eight SRAP primer combinations showing 92.29% polymorphism. Nei’s genetic diversity (H) within populations from RAPD and SRAP was 0.2303 and 0.2016 and the Shannon diversity index (I) was 0.3380 and 0.2970, respectively. Among populations, H (0.3450 and 0.3237) and I (0.5156 and 0.4852) were also surveyed. Overall genetic diversity between and within populations was high. Results suggest that in situ conservation together with the introduction of plants from different locations is recommended to increase genetic variation.
