Objective To comprehensively map the distribution patterns of native medicinal plants of Xinjiang Uygur Autonomous Region, China; To find the environmental determinants and to give suggestions for the conservation planning of medicinal plants in Xinjiang region. Methods Firstly, we compiled the distribution data of native medicinal plants at a county level in Xinjiang region, including the source plants of Chinese Materia Medica(CMM), Uygur Medicine(UM), and Kazak Medicine(KM); Secondly, we divided the distribution data into grid with a resolution of 0.1°× 0.1° and overlaid it on the topography and climate data in Arcgis 10.0; Finally, we analyzed the correlations of medicinal plant richness and environmental variables with ordinary least square(OLS) regressions and partial regressions. Results UM has more non-native species in Xinjiang region than KM. The species richness of medicinal plants is high in Altay Mountains, western Tianshan Mountains, and part of Kunlun Mountains. The richness of medicinal plants is highly correlated with the vascular plant species richness and climate, and further, the independent effects of vascular plant species richness are higher than the independent effects of climate. The whole plant, root & rhizome, and seed & fruit are more frequently used than stem and leaf for CMM in Xinjiang region. Conclusion The distribution patterns of medicinal plants are concordant with vascular plant species, which could be carefully considered in the conservation planning of this region. Taking full advantage of current nature reserves is a low-costing approach to the conservation of medicinal plants although they were not originally established for medicinal plant protection. Nevertheless, it is urgent to further study the distributions and protection status of medicinal plants in the nature reserves of Xinjiang region. Objective To comprehensively map the distribution patterns of native medicinal plants of Xinjiang Uygur Autonomous Region, China; To find the environmental determinants and to give suggestions for the conservation planning of medicinal plants in Xinjiang region. Methods Degree, we compiled the distribution data of native medicinal plants at a county level in Xinjiang region, including the source plants of Chinese Materia Medica (CMM), Uygur Medicine (UM), and Kazak Medicine (KM); Secondly, we divided the distribution data into grid with a resolution of 0.1 ° × 0.1 ° and overlaid it on the topography and climate data in Arcgis 10.0; Finally, we analyzed the correlations of medicinal plant richness and environmental variables with ordinary least square (OLS) regressions and partial regressions. Results UM has more non-native species in Xinjiang region than KM. The species richness of medicinal plants is high in Altay Mountains, western Tianshan Mountains, and part of Kunlun Mountains. The r ichness of medicinal plants is highly correlated with the vascular plant species richness and climate, and further, the independent effects of vascular plant species richness are higher than the independent effects of climate. The whole plant, root & rhizome, and seed & fruit are more frequently used than stem and leaf for CMM in Xinjiang region. Conclusion The distribution patterns of medicinal plants are concordant with vascular plant species, which could be carefully considered in the conservation planning of this region. Taking full advantage of current nature reserves is a low- Yet, it is urgent to further study the distributions and protection status of medicinal plants in the nature reserves of Xinjiang region.