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This study simulates the distributions of 13 endemic and near-endemic genera (Ammopiptanthus, Sympegma, Iljinia, Elachanthemum, Potaninia, Tugarinovia, Kaschgaria, Sarcozygium, Timouria, Zollikoferia, Stilpnolepis, Synstemon and Tetraena) to indicate areas of plant diversity and conservation importance within the eastern Central Asian desert, and to identify the determinant environmental variables contributing to the spatial distribution patterns. Using known distribution localities and 14 environmental variables, the Maxent and Domain species distribution models were employed to map the patterns of geographic distribution. The power of predictability of the models was tested using the receiver operating characteristic method and the jackknife validation approach, according to the different number of species localities available. The estimated richness and the superimposed potential distributions of 13 genera were used to indicate endemic patterns of distribution. The comparison of Maxent and Domain further identified previously unknown areas of endemism and described the distribution for each taxon. Both observed species occurrence and the species occurrence predicted from the Maxent indicated that the eastern Alashan of Inner Mongolia is the most noticeable endemic area, and the northwestern and northern Tarim Basin of Xinjiang is the secondary center of plant diversity. These regions were then prioritized for conservation importance. Potential evapotranspiration ratio and precipitation seasonality played important roles in driving the observed patterns of endemic distribution.