Abstract: The spatial pattern or structure of genetic variation within populations is an important part of evolutionary and ecological genetic processes in natural populations of plants, and may provide deep insight into the conservation of endangered species. In this paper, we investigated the spatial distribution patterns of population genetic variation of two orchid species, Paphiopedilum micranthum and Changnienia amoena , using RAPD markers. A total of 89 and 42 individuals in two populations of each of the species, respectively, were involved in our study. Based on the polymorphic bands generated by 12 ( P. micranthum ) and 16 ( C. amoena ) RAPD primers, Moran′s I spatial autocorrelation coefficient was calculated, which revealed significant spatial structure of genetic variation within populations of P. micranthum (with significant positive autocorrelation over short distance class: 3～4 m). In contrast, the genetic variation in C. amoena populations was found to be randomly distributed. The different spatial distribution patterns may be attributed to the different reproductive systems of these two species. P. micranthum undergoes significant clonal growth while no significant clonal reproduction was found in C. amoena . These results have important implications for the conservation and management of these species, especially for the sampling strategies for ex situ conservation.