A DNA-based fingerprint technique was developed for teak with 15 microsatellite markers, based on 26 widely cultivated teak clones. The same set of markers was used to investigate genetic variations and relationships of the 26 teak clones. Using the fingerprint technique, all teak clones could be unequivocally identified. In terms of genetic diversity among 26 clones, 160 alleles were detected with mean of 10.67 alleles per locus. The observed heterozygosity ranged from 0.3333 to 1.0000, averaging 0.6567. Despite the limited sample, there was substantial genetic variation that could be exploited in teak breeding programme. In addition, the cluster analysis separated teak clones of India origin from Myanmar and essentially confirmed historically known or speculated origin of the clones. Implication on clonal identification and management as well as the protection of legitimate interests of breeders and growers was discussed.