On the basin of RAPD analysis, genetic diversity and structure of the natural populations of Abies holophylla was estimated by AMOVA procedure. The average value of percent of polymorphic markers was 71.9%. Most variation existed among individuals within population(80.2%). Genetic differentiation among populations(Φ_(ST)) was 0.198. When the populations were grouped as two region(i.e., Taebaek and Sobaek Mountain Regions). 8.5% of the total genetic variation was explained as regional differences. The heterogeneity of molecular variance among populations was investigated with Bartlett`s test, which revealed that populations of Mt. Taebaek and Mt. Gariwang were more heterogeneous. Generally, the populations of Taebaek Mountain Reion were more heterogeneous than those of Sobaek Mountain Reion. Finally, the applicability of AMOVA to the populations frenetic study was discussed in comparison with other measures of genetic differentiation which were widely used.