Genetic diversity and genetic differentiation were examined in four wild populations of Carya cathayensis in southern mountainous area of Anhui Province using random amplified polymorphic DNA (RAPD) markers. As analyzed by POPGENE software, a total of 139 discernible loci were obtained from all populations using 15 random primers, 62.59% of which (87 fragments) were polymorphic loci, with an average percentage of polymorphic loci as 43.35% for all populations. At species level, Nei’s genetic diversity (H=0.124) and Shannon’s information index (I=0.208) indicated that C. cathayensis had a relatively low genetic diversity. The higher value of differentiation (G_st=0.417) and the lower value of gene flow (N_m=0.700) showed that the geographic isolation has an obvious influence among populations.