The conservation of tropical rain forests is an important issue for biodiversity and sustainability. To prevent the rapid decline of forests, selective logging systems have been used in a number of countries of Southeast Asia. We have evaluated the effect of the different silvicultural systems and/or number of cutting rotations on the genetic diversity of S. parvifolia. The results suggest that harvesting rotation of first (L1) and second (L2) (selective cutting individuals with dbh>50cm) lead to reducing genetic diversity slightly. The second rotation (L3) (selective cutting individuals with dbh>40cm) would reduce much number of reproductive trees, especially decreasing the number of rare and private alleles. The decreasing genetic diversity on the logged forests could be maintenance and improve through enrichment planting with using native species i.e. S. parvifolia. Consequently the genetic diversity of logged forests could be preserved through maintaining of harvesting individuals with dbh>50 cm. On the other hand, supplementary genetic diversity by enrichment planting collected in the primary forest could gain the genetic diversity of logged forests.