Abstract: Population genetic structure was studied using isozyme loci and phenotypic characters in five seperate clusters of masson pine (Pinus massoniana Lamb.) in Shaxian County of Fujian Province.By polyacrylamide gel electrophoresis and measuring twelve phenotypic characters,we investigated the population genetic structure of masson pine at molecular and phenotypic levels.The results were as follows: (1) The level of genetic variability in the population of masson pine,was relatively high.The percentage of polymorphic loci (P) was 64.5%±4.2%.The average number of alleles per loci (A) was 1.65±0.054.The average expected heterozygosity (H₆) was 0.216±0.0089. (2) Similar to reports for other conifers,the differentiation level of masson pine was relatively low.The average genetic distance (D) among the five clusters was 0.0047.2.4% of the allozyme variability was attributed to the differentiation among the clusters while the remaining 97.6% resided within the different clusters.The analysis of variance for the twelve phenological gharacters gave the same general trend and average genetic variation within the different clusters was 94% approximately,with same 6% resided among clusters. The aspects of population genetic structure of masson pine and some problems of isozyme analysis are discussed.