Global climate change will have great impacts on ecosystems with high biodiversity and landscape connectivity. Here, we employ species distribution models (SDMs) and geospatial analyses to predict future changes in C. thalictroides distribution under the future climate change based on Community Climate System Model (CCSM4). We predict the ranges of C. thalictroides will contract about 11,523 km(2) from the present to the year 2080. The changes in species distribution present a main range contraction in high latitude regions. We map the patterns of genetic divergence and diversity using the Genetic Landscape GIS Toolbox in ArcGIS v10.2. By visualizing dispersal networks in SDMtoolbox v 1.1, we predict a major decrease in connectivity will occur between YD (Yingde) and NP (Nanping) population. Populations with high diversity and divergence regions were considered to be evolutionary hotspots. Therefore, we suggest the populations CZ(Chengzhou), YD(Yingde), HP(Hepu), SY (Sanya), DH(Dinghu) and NP(Nanping) are in need of protection, concluding that strategically maintained ecological connectivity must be a key component of conservation strategies for C. thalictroides. We believe the creation of genetic landscape based on genetic datasets and connectivity assessment in relation to climate change will provide increasingly useful information and new implications for prioritizing the conservation of the endangered species.