Climate change poses a significant threat to the survival of many species. Although protected areas can slow down biodiversity loss, they often lack systematic planning and do not integrate genetic diversity into their design. Genetic diversity is a key prerequisite for species survival and the ability to tolerate new conditions. Using population genetic and distribution data from 96 plant species in the Third Pole (encompassing the Tibetan Plateau and adjacent mountains), we mapped patterns of genetic diversity, projected climate-driven range dynamics and future genetic erosion, and designed an optimal conservation framework for the region. We identified several patches of high haplotype diversity (HD), with a relatively high number of haplotypes in southeastern Third Pole. Regression models revealed that climate and topography have interacted to shape patterns of genetic diversity, with latitude and precipitation being the best predictors for HD of cpDNA and nrDNA respectively. Ecological niche modeling predicted an approximate 43 km northwestward and 86 m upward shift in suitable habitats under future climate scenarios, likely leading to a significant loss of up to 13.19% and 15.49% of cpDNA and nrDNA genetic diversity, respectively. Alarmingly, 71.20% of the newly identified conservation priority areas fall outside of the existing protected areas and planned National Park Clusters. Therefore, we recommend expanding the network by 2.02 × 105 km2 (5.91%) in the Third Pole, increasing the total conserved area to 1.36 × 106 km2 (39.93%) to effectively preserve the evolutionary potential of plants. This study represents an innovative attempt to incorporate genetic diversity into biodiversity conservation efforts. This data package comprises the dataset associated with the following publication: Moses C. Wambulwa, Guang-Fu Zhu, Ya-Huang Luo, Zeng-Yuan Wu, Jim Provan, Marc W. Cadotte, Alistair S. Jump, Francis N. Wachira, Lian-Ming Gao, Ting-Shuang Yi, Jie Cai, Hong Wang, De-Zhu Li, Jie Liu. (2025). Incorporating genetic diversity to optimize the plant conservation network in the Third Pole. Global Change Biology. ######################################################################################################### A detailed description of the data files is provided below. 1. The "Code" folder contains all in-house R and Python scripts used for data analysis. Specifically, the "Genetic_landscape_analysis.py" file includes code utilizing the arcpy package in ArcGIS Pro (Version 2.9.2) for analyzing genetic diversity and genetic divergence. The "Third_Pole_MetaAnalysis.R" file contains the primary analysis scripts used in this study. 2. The "Environment_Data" folder contains genetic diversity data used for statistical analysis and environmental variables at a 2.5° resolution. "cp" refers to chloroplast DNA, "nr" refers to nuclear DNA, "HD" refers to haplotype diversity, and "SR" refers to species richness. 3. The "Genetic_Data" folder contains genetic diversity and genetic divergence data for each species based on reconstructed sequence matrices of chloroplast DNA and nuclear DNA. 4. The "Haplotype_Data" folder contains recalculated population and haplotype matrices for each species, and include GPS coordination. 5. The "Identified_Protected_Areas" folder contains the 15 priority areas in the Third Pole identified in this study, and are based on genetic diversity and other data. 6. The "Occurrence_Data" folder contains distribution point data for 96 species, primarily used for species distribution modelling.