Indigenous medicinal plants have gained attention worldwide for their ability to cure different ailments. However, there are concerns over the contamination of these plants by fungal species, which produce mycotoxins. This study investigated 36 different medicinal plants purchased from Faraday Muthi Market, Johannesburg, South Africa for fungal contamination using macro- and microscopic approaches, and their identities were confirmed by molecular means. The fungal loads of the mycoflora recovered from the medical plants ranged from 1.8 × 104 CFU/g to 2 × 107 CFU/g, exceeding the WHO regulatory limit of 1 x 103 CFU/g. Furthermore, a total of 164 fungal species from nine genera, including Aspergillus (39.6%), Penicillium (19.5%), and Fusarium (9.7%), other notable fungal genera such as Alternaria (5.5%), Mucor (5.4%), Rhizopus (5.4%), Chaetomium (4.2%), Cladosporium (3.6%), Emericella nidulans (3.6%) and Epicoccum (3.0%) were also recovered from the medicinal plants. Furthermore, A. niger (10.97%) was the most prevalent among all the identified fungal species. Consequently, consuming fungal-contaminated medicinal plants may increase the risk of exposure to fungal species, which might have a dire impact on human health. Therefore, this research underscores the importance of stringent quality control measures in the cultivation, harvesting, and processing of medicinal plants in South Africa and other African countries to mitigate fungal contamination risks.