Abstract: The mating system of natural population in Pinus bungeana was analyzed by applying isozyme starch gel technology, and the outcrossing rates of multilocus was 0.451～0.522, which standed at lower level compared with other pines and which was accordant to its lower gene flow and heterozygosity. The reasons leading to lower outcrossing rate were discussed. The genetic differentiation coefficient of family reached to 0.322, which was higher than that of population. The genetic variation among natural populations, half-sib families, and progeny individuals within half-sib families counted up 0.133, 0.279 and 0.588, respectively. The genetic diversity proportion of the three levels equaled approximately 1∶2∶4. The results provided an important basis for tree breeding and gene conservation in Pinus bungeana.