A study was conducted in Eastern Kenya to assess incidence and severity of Adansonia digitata and Sclerocarya birrea diseases under seasonal variations, and to assess associated fungal genera and their distribution. Asymptomatic and symptomatic tissues were sampled from 175 randomly selected trees. Isolations were done from leaves, twigs and bark following laboratory standard procedures. Samples were plated on Malt Extract Agar (MEA) and incubated at 25^oC for 7 days. Fungal colonies were evaluated, and pure cultures were obtained using a single hypha. Fungal pathogens were identified based on morphological characteristics of cultures and spores. Statistical analysis were done using GENSTAT version 18. Fungal morphotypes isolated included: Pestalotia (39.0%), Botryosphaeria (41.0%), Fusarium (12.0%), Alternaria (7.9%) and Cladosporium (0.1%). There were no stastically significant differences (p<0.01) in number of isolated fungi among different plant samples and sampling locations. This is the first detailed study on fungal diversity associated with diseased and healthy A. digitata and S. birrea trees in Kenya and it clearly indicates the need for detailed studies of fungal species isolated to develop mitigation strategies.