Abstract: The genetic diversity of ten populations of Sophora moorcroftiana in the middle reaches of the Yarlung Zangbo River, Tibet, China was assessed using allozyme analysis by horizontal sliceable starch gel electrophoresis. Twenty four loci (46 alleles) of 13 enzyme systems demonstrate low levels of genetic variation within populations, with the value of P_p＝25.0%～37.5%,A_p＝1.3～1.7 and H_ep=0.112～0.169. At the species level, the genetic diversity of S. moocroftiana (P_s=37.5%, A_s=1.9, H_es=0.171) was lower than the mean value of angiosperms of long lived woody species (P_s=59.5%,A_s=2.10,H_es=0.183). Wright′s F statistics analysis indicated that F_IS, a measure of the deviation from random mating within the 10 populations, was -0.0071, suggesting deviation from Hardy-Weinberg equilibrium and a slight heteroygote excess in some populations. The higher level of differentiation (F_ST＝0.1748) among populations than those of other long lived woody plants may result from habitat fragmentation and low levels of gene flow (N_m=1.1802) caused by environmental deterioration and human disturbance, including over felling and over-grazing. It was worth noting that populations H2 (Xietongmen), H31 (Jiangdang1), H32 (Jiangdang2), and H5 (Langsailing) harbored the majority of alleles and had high levels of genetic diversity, suggesting that these populations in particular should be conserved in situ.