Pinus bungeana is a three-needle pine with typical fragmented distribution in central and northwestern China. Its natural resources are gradually decreasing and need to be conserved. For conserving genetic diversity of P. bungeana, the authors sampled 10 natural populations in its distribution areas and conducted the analysis of isozymes. Thirty one loci with 53 alleles on the basis of 16 enzyme systems were assayed. The parameters of genetic diversity at species and population level are respectively as follows: As= 1.742, Ae[s] = 1.49, Ps= 54.8%, He[s] = 0.162, Ap= 1.39, Ae[p]= 1.30, Pp= 34.85, He[p] = 0.0986. In comparison with other pines, P. bungeana possesses a slightly low amount of genetic variation especially at the population level. By contrast, the level of population genetic differentiation (GST = 0.135) is higher compared to other pines. All ten populations are divided into three groups according to Nei's genetic identity (I). There is a slight relation (r = 0.31) between genetic distance and geographical distance.Some populations are obviously deviate from Hardy-Weinberg equilibrium but the total population is basically accordant with Hardy-Weinberg equilibrium. The correlation analysis between allele frequencies and ecological factors showed that the alleles at loci of Idh and Pgi-2 had gradient variation trends of their frequencies. The sample capturing curves' analysis indicated that the captured alleles increased when the number of sampled populations increased and 99% out of whole allele pool of ten populations would be captured when five populations were randomly selected. At last,. the population genetic structure of P. bungeana and its conservation strategy were discussed.