Abstract: Thirty trees of Malus xiaojinensis randomly sampled from three natural populations in two distribution areas (about 50 kilometers apart) , i. e. Dengcun of Mopo and Lianghe townships , Xiaojin County , Sichuan Province , and thirty corresponding seedlings were analyzed using random amplified polymorphic DNA (RAPD) techniques. Based on statistical analysis of the 81 RAPD bands produced by 15 decamer primers in polymerase chain reactions (PCR) with all of the DNA samples studied , the number of polymorphic RAPD bands among all the individuals and different populations were counted. The genetic relationship among all the individual trees and between different populations were analyzed using Nei and Li (1979) genetic distance and neighbor-joining methods in the TREECON software package. Genetic variance analysis was carried out using the AMOVA method in Arlequin Ver. 2. 000 software package. From 15 random decamers , 81 polymorphic bands were produced in all the DNA samples studied , average 3. 8 bands per primer. The average polymorphic RAPD bands of both three existing populations and their corresponding descendent seedling populations were about 1. 5 per primer. Among them , the highest average polymorphic RAPD bands per population is 2. 5 and the lowest is 0. 7. The genetic relationship trees constructed by the TREECON computer program for all the individuals and different populations show that there is genetic differentiation among the populations of M. xiaojinensis . The AMOVA analysis indicates that the seedling population variances composed a large part of the species genetic variation of M. xiaojinensis .