Saraca asoca
(Roxb.) De Wilde is an important medicinal plant from the Western Ghats of India, traditionally used in treatment of various gynecological disorders. Increasing commercial demand and decreasing numbers has resulted in this plant becoming endangered with crude drug materials being extensively substituted/adulterated with other plant species. The present study was undertaken with the objective of development and evaluation of multivariate cluster analysis of ISSR fingerprints againstrbcL-based DNA barcodes as tool to understand the relationships and to differentiate common adulterants and substituents fromS. asoca. ISSR-based Hierarchical Cluster Analysis was carried out on 41 samples ofS. asocaand 5 each of the 5 common substituent/adulterant plants and the clustering patterns were evaluated against DNA-sequence-based barcoding ofrbcLregion of their plastids. Factorial analysis and Principal Coordinate Analysis revealed distinct groups of genetic pools of respective taxa thereby confirming the utility of ISSR fingerprinting as a useful tool for differentiation between the genuine and the adulterants/substituents. NCBI-BLAST search on DNA barcoderbcLregion confirmed the results of ISSR assays. Therefore, our study demonstrated the utility of simple, cost-effective method of ISSR fingerprinting coupled withrbcLbarcoding in differentiating this important medicinal plant from its common adulterants/substituents.