Prince Rupprecht's larch (Larix principis-rup-prechtii Mayr.),a deciduous conifer,widely grows in middle and high elevations of Northern China.Its natural distri-bution has sharply decreased and has become fragmented,which may have resulted in the loss of genetic variation.In this study,ten natural populations across the entire range of this species were analyzed using amplified fragment length polymorphism markers.A total of 309 loci were detected from 225 individuals of these populations,of which 261(84.5％) were polymorphic.At the species level,the genetic diversity was high (average of the Nei's genetic diversity He= 0.2602,and Shannon's information index I= 0.3967).The results of molecular variance analysis showed that 90.71％ of the genetic diversity occurred within populations.The genetic differentiation among populations was moderate as a whole (FST= 0.0929,GST=0.1510),which is consistent with the moderate level of gene flow among populations(Nm = 2.8116).Based on the unweighted pair group method with arithmetic mean and STRUCTURE analysis,these pop-ulations were grouped into three genetically distinct clusters.The degree of inter-population differentiation (GST= 0.1338)for the south group was larger than that for the north group(GST=0.0915).There was a significant correlation between genetic distance and geographic distance across the species range (r = 0.316,P＜0.05).Genetic diversity was signifi-cantly associated with longitude but not elevation or climatic factors.The populations with high genetic diversity from each cluster are therefore recommended for future conserva-tion and management of this species.