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The genetic diversity within and among populations of Shorea leprosula and Shorea parvifolia from Indonesia was investigated using amplified fragment length polymorphisms (AFLPs). The results indicated that S. leprosula is genetically more variable than S. parvifolia. At the population level, a higher level of genetic diversity was revealed for S. leprosula with a percentage of polymorphic loci (PPL_p) of 53.32% and an expected heterozygosity (H _ep) of 0.16 in comparison with S. parvifolia showing PPL_p of 51.79% and H _ep of 0.14. At the species level, S. leprosula showed PPL_s of 92.86% and H _es of 0.21, while S. parvifolia showed PPL_s of 85.71% and H _es of 0.21. Genetic differentiation (G _st) indicated that 25 and 31% of total genetic diversity in S. leprosula and S. parvifolia, respectively, were attributed to the differences among …