Multilocus expressed sequence tag-based simple sequence repeat (EST-SSR) genotypes of 724 individuals of Shorea leprosula used in the publication. Samples were collected in the natural populations of Malay Peninsula, Sumatra and Borneo and a plantation forest in Java. The data are in a format suitable for the program GenAlEx (Peakall and Smouse 2006). The first line includes no. of loci (27), no. of individuals (724), no. of populations (24) and sample sizes of each population (18, 21, 19, ...). The second line includes the names of study species and each population. Third line includes the names of each locus. PCR product sizes for each individuals are described below the third line. Please note that eight FST-outlier loci (Tum1403A11, Tum1406G13, Tum1602L21, Tum0303D01, Tum0309D20, Tum1602G19, SleE13 and SleE16) were excluded from the population genetic analyses conducted in the publication.