Abstract: Ammopiptanthus nanus is an endangered evergreen shrub endemic to the deserts of central Asia and plays an important role in delaying further desertification. We examined allozyme variation and AFLP diversity in A. nanus populations and investigated the mating system of this species using progeny arrays assayed for polymorphic allozyme loci. Mating system analysis in the Keyi'eryongke'er population showed low levels of out-crossing, and strong inbreeding depression. Low levels of genetic variation were detected at both population (allozyme, P_p= 14.0%, A= 1.14, H_e= 0.031; AFLP, P_p= 14.5%, Shannon's information index I= 0.063) and species (allozyme, P_p= 21.1%, A= 1.21, H_e= 0.040; AFLP, P_p= 20.9%, I= 0.083) levels; while moderate genetic differentiation existed among populations, as indicated by allozymes (G_ST= 0.081) and AFLP (G_ST= 0.151–0.193). Founder effect, bottlenecks in evolutionary history, the mixed mating system and co-ancestry may have influenced the level of genetic diversity in A. nanus. Markers of both types provide new insights for conservation management, indicating that the Biao'ertuokuoyi and Keyi'eryongke'er populations should be given priority for in situ conservation and regarded as seed sources for ex situ conservation.

Key words: AFLP, allozyme, Ammopiptanthus, conservation, endangered plant, genetic structure, outcrossing rate