Central Asia is one of the major arid regions of the world, and the spatial genetic structure of plant species in this area displays broad significance with respect to the understanding of plant evolution and biogeographical patterns of temperate arid lands. Although the genetic structure of some plants has been examined in previous studies, it remains mostly unconfirmed whether different plants in the same habitat have similar genetic structure, and the factors that have influenced structure in plants of the region are also unknown. Accordingly, we employed the approaches of molecular phylogeography and species distribution modelling to compare spatial genetic structure and ecological niches for three montane forest and four lowland xerophytic plants in East Central Asia. The results obtained suggest that the three forest species retreat westward during the Last Glacial Maximum as indicated by higher genetic differentiation in western populations. By contrast, multiple peaks of genetic differentiation were detected from chloroplast DNA datasets among populations in each of the four xerophytic species. Based on nuclear ribosomal internal transcribed spacer datasets, anemophilous pollination had shaped the high dispersal ability for pollen-mediated gene flow and outcrossing pollination had triggered extensive heterozygosity among populations. In conclusion, palaeoclimatic changes and species traits have mainly influenced the spatial genetic structure of forest and xerophytic plants in arid Eastern Central Asia. (C) 2016 The Linnean Society of London.