Abstract: Pinus bungeana is an endemic pine with typical fragmented distribution in central and northwestern China. Its genetic diversity is gradually decreasing and needs to be conserved. For strengthening its genetic resources conservation, ten populations were sampled in the main distribution areas of Pinus bungeana and studied by starch gel electrophoresis on 16 enzyme systems. On the basis of analysis of allozyme bands, 31 loci and 53 alleles were coded, among which, there were 32 essential genes, 14 widespread genes, six sporadic genes and one unique gene. Differences exist in the number and type of genes among populations. The central population P4 had the largest number of genes, and the marginal populations P1, P7 and P10 had the least, but they had more rare and unique genes. Sampling capture curve analysis indicated that the captured genes increased when the sampled populations increased, and 99.9% out of the whole gene pool of ten populations would be captured when five populations were randomly selected. Correlation analysis showed that gene frequency on loci Idh and Pgi^-2 had gradient variation trends which were in accord with most of the phenotypic characteristics. This study provides the basis for gene conservation in natural populations of P. bungeana.