Endophytes are widely defined as all organisms inhabiting plant organs that at some time in their life can colonize internal plant tissues without causing apparent harm to the host. These reside mostly in indigenous plant host. Indigenous plants play an important role in the ecosystem, be it by providing food or shelter to other organisms in the area or by maintaining an ecological balance. However, attack by parasitic fungi may have devastating effects. This study focused on determining the identity of endophytic fungal species associated with marama bean leaves in Otjiwarongo area. Marama is being considered for domestication for its highly nutritional value and because it grows well in dry areas. Healthy looking Marama leaves were collected for analysis, but seven months later, endophytic fungal infection was observed on leaves. Pure fungal cultures were obtained from single spore of the fungi and DNA was isolated from fungal mycelium and used as templates in PCR amplification of internal transcribed spacer (ITS) region. The amplified ITS products were electrophoresced on agarose gel and sequenced in an automated sequencer. Basic Local Alignment Search Tool (BLAST) revealed the identity of the fungi as; Phoma sorghina, Penicillium commune, Alternaria tenuissima, and Alternaria alternata. Marama is in the process of domestication, therefore it is vital to assess its natural tolerance to pest and pathogens for its eventual success as a crop.