Enriched genomic libraries in GA and GT tandem repeat motifs were generated from rubber tree (Hevea brasiliensis). Design of appropriate primer pairs in the flanking regions enables to produce amplified fragments for 310 of these sequences. The test of these genomic microsatellites on a set of 10 rubber tree genotypes allows the characterization of 296 new polymorphic markers. Expected heterozygosity ranged from 0.10 to 0.93 and allele numbers from 2 to 11. Microsatellite loci with GA motifs were more abundant, longer and more polymorphic than GT motifs. Such a high variability suggests the utility of these markers for the establishment of integrated linkage maps, as well as the characterization of linkage disequilibrium in rubber tree populations.