Understanding genetic variation and structure, adaptive genetic variation and its relationship with environmental factors is of great significance to understand how plants adapt to climate change and design effective conservation and management strategies. The objective of this study was to (I) investigate the genetic diversity and structure by AFLP markers in 36 populations of R. aureum from northeast China, (Ⅱ) reveal the relative contribution of geographical and environmental impacts on the distribution and genetic differentiation of R. aureum; (Ⅲ) identify outlier loci under selection and evaluate the association between outlier loci and environmental factors and (Ⅳ) exactly calculate development trend of population of R. aureum，as it is confronted with severe climate change and to provide information for designing effective conservation and management strategies. We found high genetic variation (I = 0.584) and differentiation among populations (ΦST = 0.711) and moderate levels of genetic diversity within populations of R. aureum. A significant relationship between genetic distance and environmental distance was identified, which suggested that the differentiation of different populations was the caused by environmental factors. Using BayeScan and Dfdist, 42 outlier loci identified and most of the outlier loci are associated with climate or relief factors, suggesting that these loci are linked to genes that are involved in the adaptability of R. aureum to environment. Species distribution models (SDM) showed that climate warming will cause a significant reduction of suitable area for R. aureum especially under the RCP 85 scenario. Our results help to understand the potential response of R. auruem to climatic changes, and provide new perspectives for R. auruem resource management and conservation strategies.