Oroxylum indicum (L) Vent (Bignoniaceae) is an important but endangered medicinal plant of Western Ghat region. It is also found in North east region and in foothills of Himalayas. In the present study, Inter Simple Sequence Repeat (ISSR) and Random Amplified Polymorphic DNA (RAPD) were employed to investigate the genetic diversity of the plant Oroxylum indicum L (Vent) collected from four different locations. 5 RAPD and 15 ISSR markers were used to compare and predict the genetic similarity or differences within accessions analysed. Eight ISSR primers together produced 64 bands across four genotypes, of which 28 bands were polymorphic showing 43.89 % polymorphism. The results show that the variation among populations or geographic region is more prominent and divided the plants region wise indicating the role of geographic isolation in shaping the present population genetic structure. This distributive pattern of genetic variation of Oroxylum indicum (L) Vent accessions provides an important baseline data and implies that the conservation efforts should aim to preserve this endangered species of Western Ghats.