Abstract: We have studied genetic structure of natural population in masson pine (Pinus massoninan Lamb) using isozyme clcctronphorsis method. 12 loci of 3 enzyme systems (GOT, MDH and GDH) of seed endosperm samples coming from 6 populations were analysed. The results were as follows: the level of genetic varibility in the population of masson pine was relatively high. There were excesses of homozygotcs and deficiencies of hctcrozygotcs within population.Masson pine populatoin wasn’t under Hardy-Wcinbcrg equilibrium. The differentiation level of masson pine was relatively low. About 9% gene diversity was attributed to the differentiation intcrpopulation while ninety-one percent of the total gene diversity resided within population. The relationship between geographic distance and genetic distance of population appeared to be weak. There was significant heterogeneity difference among three populations of Guangxi and populations Guangdong, Fujian and Guizhou. In this paper, the author also suggests the strategy of masson pine genetic improvement.