Understanding of genetic diversity is very important for the management of conservation in any endangered species. Vanda thwaitesii Hook.f. and V. wightii Rchb.f. are two notified endangered orchids of Western Ghats, India demanding evaluation of genetic diversity for conservation action and thus presently, these studies have been carried out. ISSR profile of 20 samples from 15 populations of Vanda thwaitesii in a spatial separation of 10-286 km from type locality exhibited very low heterozygosity (h=0.083) and reduced gene flow (Nm=0.01). The populations clustered into 3-4 groups without any correlation between geographic locations of plant distribution. Twenty eight samples of V. wightii from 15 distinct populations separated by 40-264 km from type locality revealed moderate diversity (h=0.25; Nm=0.98) but not having correlation with respect to geographical separation. Occurrence of majority of populations in highly fragmented habitats, low levels of genetic diversity and reduced/negligible gene flow shows the immediate requirement of conserving V. thwaitesii. In spite of the existence of moderate diversity, distribution of diversity amongst the populations in disturbed forests and inhabited land necessitate the rehabilitation/reinforcement of V. wightii into protected forests.