Abstract: Background and Objective: In nature, plants incorporate a wide scope of restoratively esteemed bioactive compounds. The fungal endophytes are the organisms which grow inside the plant parts such as roots, stems, leaves and flowers and produce similar bioactive compounds of medicinal significance. The fungal endophytes from the plant Plectranthus amboinicus were not well explored in West Malaysia. Therefore, this study was designed with the objectives to harness novel endophytic bioactive compound producing fungal strains from this plant. Materials and Methods: Screening for fungal endophytes was performed by using surface sterilisation method. Sterile explants were placed on a potato dextrose agar (PDA) plates and incubated under 28°C. These fungal endophytes were identified microscopically by lactophenol-cotton blue staining protocol and molecular characterization was performed by amplification of randomly amplified polymorphic DNA tool. Results: A total of ten fungal endophytes were isolated and identified. The prevalent endophytic fungal strain found was of Penicillium chrysogenum in comparison with Aspergillus niger, Fusarium oxysporum and Alternaria solani. Therefore, these strains selected for assessment of genetic diversity. Conclusion: The most prevalent bioactive compound producing fungal strain found was of Penicillium chrysogenum associated endophytically with the plant Plectranthus amboinicus.