The present study was made an attempt to differentiate clonal variation of teak clone samples by using RAPD technique. A total of 10 different primers were used to identify the polymorphic variations between the clones. The results of the phylogenetic tree showed the highest genetic diversity (0.93) between the clones of Kerala and Tamil Nadu teaks and the lowest genetic diversity (0.53) was identified between Thaunakadavu clones of TNT 1 and TNT 2 and the results of the present findings could be further useful for the long term breeding of potential teak plants.