A combination of directed amplification of minisatellite DNA (DAMD) and random amplification of polymorphic DNA (RAPD) primes were used to assess the genetic variation within and between three isolated populations of Indian sandalwood (Santalum album). Eleven primers used in this study amplified 65.99 % polymorphic bands. Analysis of molecular variance revealed a high genetic variation among these populations (φ ST = 0.549). There are indications of clonality within the existing Indian sandalwood populations which can be attributed to habitat fragmentation, isolation and vegetative reproduction.