Genus Rosa belongs to the family Rosaceae, and comprises 100 species with a lot of popular ornamental and medicinal plants. Roses are usually utilized as an antioxidant, anti-inflammatory, antimicrobial, sleep aid and in skin diseases. This study aimed to explore the macro-and micromorphological botanical features of the stems and leaves of three Rosa varieties; Rosa banksiae var. banksaie Ait. (Bankasian Rose) (RBW); R. polyantha Thunb. ‘orange fairy' (RPO) and R. polyantha Thunb. ‘white fairy' (RPW) together with DNA fingerprinting utilizing RAPD-PCR assay and Hierarchal Clustering Analysis (HCA) for the DNA results. The three varieties share the common characters of family Rosaceae viz. compound leaves, colored flowers, and anomocytic stomata while they differ in the color of their flowers, leaflets size, the number of leaflets, and their shapes and types of calcium oxalate. RAPD assay was utilized to differentiate the three varieties genetically where primers OP-P-8, OP-P-10, OP-P-11, OP-P-12, and OP-P-14 showed the highest degree of similarity between RPO and RPW. HCA revealed the closeness of the two polyantha roses forming one cluster in the resulting dendrogram which differentiated them from the Bankasian rose. DNA assay and chemometric analysis were in accordance with the botanical profiling.