Abstract:A laboratorv analysis of isozyme phenotype for five natural populations of Pinus massoniana showed that there was an irregular variation in the frequency express of Aap-1d gene in Aap-1 loci among trees with different levels of growth vigour,in comparison with the standard trees in the sampled plots,the dominant trees had lower average frequencies. Through canonical discriminant analysis,all the sampled individual trees could be distinguished as two groups by frequency express of gene Aap-1d in Aap-1 loci,one group comprised the individuals with Aap-1d gene, the other with no Aap-1d. The analyses of variance was made for tree height and DBH based on the two groups and the results indicated that significant differences existed in the height growth but DBH. A conclusion could be drawn that height growth of this species was correlated with Aap-1d genes interlocking other genes which affected negatively the height growth of trees.