Adenium obesum, or desert rose, is a member of the Apocynaceae family and is highly valued in horticulture for its ornamental appeal and resilience in container cultivation. The current study employed Inter Simple Sequence Repeat (ISSR) markers to explore the genetic diversity of 20 distinct Adenium genotypes. ISSR markers help to identify genetic differences by targeting repeating DNA regions across the genome and they are easy to use, cost-effective and do not require prior genome information, making them useful for studying diversity in many types of organisms. In this study, ISSR analysis revealed a high level of polymorphism (81.51 %), demonstrating significant genetic variability. A total of 206 loci were identified using 25 primers, showcasing the genetic richness of the Adenium species. The genetic relationship between the genotypes was further analyzed through the Unweighted Pair Group Method with Arithmetic Mean (UPGMA), a clustering technique that grouped the genotypes based on their genetic similarities, revealing clear genetic differentiation and confirming the robustness of ISSR markers in genetic diversity studies. In addition to the genetic analysis, Gas Chromatography-Mass Spectroscopy (GC-MS) analysis of the ethanolic leaf extracts of Adenium obesum revealed the presence of 30 bioactive metabolites, including commonly identified compounds such as vitamin E, phenol, phytol and n-hexadecanoic acid. These results identified several bioactive compounds with potential medicinal properties, underscoring the pharmacological significance of the plant. Overall, this study demonstrates the effectiveness of ISSR molecular markers in both genetic evaluation and the identification of bioactive compounds in Adenium species.