Introduction Cassia L. is a large genus of the family Fabaceae, subfamily Caesalpinioideae with over 300 species distributed worldwide that commonly grows in all types of ecological sites in arid regions of India over a large area in all types of ecological sites. Species of Cassia are valued for their medicinal properties and industrial value. In Cassia the biomass production rate is very high and it is commonly used for firewood. The extensive variability in its growth habit ranging from tall trees to delicate annual herbs, numbers and size of the leaflets, form and foliar characteristics has added difficulties to taxonomists in identification of species or the intraspecific taxa for influence of habitat conditions (1). Some exotic species like C. grandis, C. laevigata, C. multijuga, C. nodasa, C. renigera and C. speciosa are grown as garden plants for their graceful appearance and beautiful flowers. All of them exhibit excellent drought resistance. This immense natural variation in Cassia may be harnessed to enhance the yield products like gums, tannins, proteins, carbohydrates and oils, biological nitrogen fixation and resistance to biotic and abiotic stresses (2). Hence, cataloging and characterizing the genomes in terms of DNA markers is of immense importance and can serve as a DNA database for future improvement programs.