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Tecomella undulata (common name Rohida) is a species of monotypic genus in Bignoniaceae found growing in arid regions of the world. Plant is known for its ornamental and medicinal use. The plant is a small or medium sized tree bearing flowers in three different colors and is presently included in the category of endangered plants in India. Three morphotypes based on flower color have been recognized in it i.e., red flowered Rohida (RFR), orange flowered Rohida (OFR) and yellow flowered Rohida (YFR). The plants were investigated cytogenetically and at a molecular level to detect the variability. Cytological investigation showed that all the plants possess the chromosome number of n=18 irrespective of the morphotype studied with high pollen fertility. The molecular diversity studies were carried through a random amplification of polymorphic DNA (RAPD) analysis. Amplification of genomic DNA of ten accessions of T undulata using six RAPD primers yielded 87 fragments out of which 75 were polymorphic. The RAPD bands obtained from six primers were finally used to infer genetic distance between the morphotypes. OFR accessions had higher genetic diversity with the Nei’s expected heterozygosity (h)=0.266, Shannon’s information index (1)=0.388 and percentage polymorphism of 62.52%. The present study concludes that though the plant showed same chromosome number, intraspecific variability exists in T undulata that has a molecular genetic basis. The genetic information can be used for proper conservation of the plant besides being used as a tool to select plants for breeding purpose.