Endophytes are bacteria or fungi which live inside the host plant and participate in many biological processes without causing disease or other adverse effects. Endophytes are recognised as a rich source of secondary metabolites with potentially useful pharmacological properties. Many South African medicinal plants are highly under-investigated sources of potentially useful endophytic microbes. In this report six endophytic fungi were obtained from the leaves, stems and roots of South African medicinal plants which are known for their traditional uses and pharmacological properties. The endophytic fungi were isolated from Cotyledon orbiculata L., Psychotria zombamontana (Kuntze) Petit, Tecomaria capensis (Thunb.) Lindl., Catha edulis (Vahl) Endl. and Melianthus comosus Vahl. The crude extracts of the isolated endophytic fungi were investigated for their antimicrobial potential, extracellular enzymatic activity and phosphate solubilization. Additionally, the present study used genetic screening to assess the ability of the endophytic fungi to synthesize bioactive compounds, indicated by the presence of the polyketide synthase type 1 (PKS 1) gene. In preliminary microbial inhibition screening the fungal extracts had promising antifungal activity against Cryptococcus neoformans and Candida albicans. Furthermore, the endophytic fungus Talaromyces funiculosus displayed extracellular enzymatic activity, namely xylanase and cellulase. Five fungal strains demonstrated ability to solubilize phosphate and three strains demonstrated the presence of polyketide synthase type 1 (PKS 1) gene. It is worth considering further investigation of their bioactive secondary metabolites.