Abstract: Ammopiptanthus nanus is a rare and endangered species,native to desert habitats in Northern China.Allozyme diversity and population differentiation were evaluated for six natural populations using isoelectric focusing in thin-layer polyacrylamide slab gels.A total of 19 loci from eight enzyme systems were detected.An extreme low level of genetic variation was revealed both at the species level(A=1.21,P=21.05%,H_e=0.040)and at population level(P=14.04%,A=1.14(0.04),H_e=0.036(0.018)),which were lower than those of long-lived perennial woody and narrowly distributed species.Wright’s F-statistics analysis indicated a deficit of heterozygote both at population level(F_IS=0.129)and at the total population level(F_IT=0.202).A low level of genetic differentiation among populations detected(F_ST=0.085)was consistent with a high level of genetic identity among the populations(I=0.997).The history of bottleneck effect was speculated to be the main course for the current genetic structure in A.nanus.Consequently,conservation concerns of this species were discussed and conservation recommendations are suggested based on the results obtained from the study.Consequently,conservation of Keyieryongker(KE)population which maintained high genetic variability is recommended and this population could act as a source of transplant.