Bananas (Musa spp.) are major staple and cash crops in the Great Lakes region of Africa. Yet, banana yields in this region are among the lowest in the world due to a wide range of abiotic, biotic and socioeconomic causes. Cropping systems which could contribute to soil fertility replenishment, pest and disease suppression and climate change mitigation might improve banana yields and contribute to uplifting the livelihoods of millions of people in the region. In this context, a survey was conducted over two seasons in banana-based subsistence farming systems in Rwanda, Burundi, north-western Tanzania (Kagera and Kigoma regions) and eastern Democratic Republic of Congo (South Kivu province), to\n investigate the distribution and incidence of banana Fusarium wilt as related to cropping systems, edapho-climatic and socio-economic factors. Banana Fusarium wilt incidence was found generally high in the region, 54.1% of all farms had disease incidence higher than 40%, with Tanzania having the highest number of farms with high disease incidence (63.6%). Statistical analysis (chi-squared test of association) and GIS mapping, by layering Fusarium wilt incidence over selected predictor maps, showed that disease incidence was lower in farms growing cultivar mixtures (p < 0.01) and at higher altitudes (>1600masl) (p < 0.05), and a significant association of Fusarium wilt and farm age was observed whereby disease incidence was highest in farms aged between 10 and 30 years (p < 0.05). Additionally, this study reports for the first time the occurrence of Fusarium oxysporum f. sp. cubense race 2 in Rwanda and Burundi, and\n suggests that strategies for banana Fusarium wilt management in east and central Africa should include raising farmers’ awareness on pathogen spread mechanisms and enhancing their access to disease-free planting materials.