Drought-tolerant multipurpose fruit trees Vangueria infausta (Burch) subsp. rotundata (Robyns) and Berchemia discolor (Klotzsch) Hemsl are native to Kenya. These fruit tree species are suitable for dryland agroforestry and support local communities with food, medicine, fodder and other necessities. Reports by the local communities indicate that the two species suffer from diebacks and cankers. The aim of this study was to identify the fungi associated with V. rotundata and B. discolor and determine the cause of diebacks and cankers symptoms observed. Samples were collected from two sites (Tiva and Ikanga) in Kitui County and one site (Mkange) in Makueni County. Fungal isolations were carried out by incubating the samples on malt extract agar media supplemented with Streptomycin Sulphate. Morphological identification grouped the fungal isolates into 7 clusters. Botryosphaeriaceae and Nectriaceae had the highest frequency of occurrence (32.7 and 30.5%) respectively. DNA was extracted from pure fungal cultures, amplified and sequenced. Phylogenetic analysis of DNA sequences clustered the fungal isolates into seven families; Botryosphaeriaceae, Sporocadaceae, Nectriaceae, Trichosphaeriaceae, Pleosporaceae, Diaporthaceae and Glomerellaceae. Using Koch's postulates, this study showed that isolates of Botryosphaeriaceae within the genera Lasiodiplodia, Alanphillipsia and Dothiorella are pathogenic to B. discolor and other indigenous agroforestry species due to their ability to cause similar symptoms to those observed in the field. This is the first study to investigate the fungal flora linked to V. rotundata and B. discolor dieback and canker diseases.