Genetic diversity of Karanja accessions were evaluated with Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeats (ISSR) markers. In present study low level of genetic diversity was observed among the karanj genotypes. Average RPI, PIC and MI value for RAPD primers were 2.09, 0.25 and 18.06 respectively; while for ISSR marker it was 0.66, 0.08 and 4.48 respectively. Genetic diversity analysis by Isozyme marker viz., POX (peroxidase), PPO (polyphenol oxidase ), EST (esterase) and SOD(superoxide dismutase) scores total 19 isozyme loci in 30 accessions of Karanja. Highest loci was scored by PPO (6 loci) followed by POX (5 loci) while 4 loci scored by SOD and EST. Highest polymorphism and highest number of polymorphic loci was shown by PPO isozyme (83.33%) while lowest polymorphism and lowest number of polymorphic loci was shown by SOD isozyme (50 %). In morphological characterization, in terms of height, tallest tree and average longest branch was recorded by NAUK-15 and NAUK-16 respectively. Average highest number of branches and largest leaflet width was recorded by NAUK-9 while longest leaflet length recorded by NAUK-1.