Chili pepper (Capsicum frutescens) cultivation plays a significant socio-economic role in Burkina Faso but is severely impacted by fungal diseases. Hence, this study evaluated farmers' disease management practices and identified the primary pathogens involved. Surveys were conducted with 30 farmers across three regions. Isolates from diseased plant parts were characterized based on morphological and molecular traits, as well as in vitro inoculations on detached leaves. Results revealed that 94% were men, with 65% being illiterate a limitation affecting the adoption of new agricultural techniques. Farmers predominantly used commercial seeds, synthetic fungicides, and insecticides, alongside crop rotation and mixed fertilization. However, their knowledge of fungal diseases was limited, with difficulty distinguishing fungal infections from bacterial or viral diseases. Common symptoms included leaf yellowing, necrosis, drying, and fruit rot. Pathological analysis identified 12 fungal genera, including Fusarium (34%), Colletotrichum (14%), Alternaria (9%), and Rhizoctonia (9%). Blast analysis of consensus sequences in ITS region indicated major isolates closely related to Alternaria porri, Colletotrichum capsici, Lasiodiplodia theobromae, Fusarium incarnatum, and Rhizoctonia solani. All five species were pathogenic on inoculated leaves and fruits, with variations in aggressiveness, some causing extensive lesions within days. This study underscores globally recognized fungal pathogens affecting chili peppers and highlights producers' reliance on pesticides despite limited disease knowledge. Promoting sustainable, participatory management strategies is critical for improving phytosanitary control and optimizing yields.