Brown blotch disease caused by Colletotrichum capsici, is one of the most important disease affecting cowpea production in Burkna Faso. Every year the disease can cause yield losses as high as 42 to 100% on farmer's fileds. This study aimed to understand the inheritance of its resistance in cowpea and also identify quantitative trait loci (QTL) associated with the resistance. Seedlings of parents and F 1 , F 2 and BC 1 F 1 progenies from crosses involving four susceptible and four resistant parents were screened in greenhouse conditions for brown blotch disease reaction. The inheritance studies indicated that different genes action were involved in the resistance of brown blotch resistance disease. In KN-1 variety, two or several genes associated to brown blotch were suggested. In Donsin local, a partially dominant gene, Rcc1, would be associated with the resistance. In Moussa local, a single major dominant gene, Rcc2, was identified. A single major recessive gene, rcc2, was found to control resistance with brown blotch in the cowpea resistant variety IT93K-503/46-13. The research of gene or QTL associated with brown blotch in cowpea variety KN-1 has been investigated. Polymorphic single nucleotide polymorphisms (SNP) markers and QTL associated to brown blotch resistance were discovered from 63 F 2 individuals from a cross involving the susceptible variety Tiligre and the resistant KN-1. More than 11800 polymorphic SNP markers covered 1019.3 cM of the whole genome of cowpea were identified. A single dominant QTL, nomed qBBDR2 and 102 individual SNP markers tightly associated with the resistance of C. capsici were identified on chromosome 2 (Phytozome) of the cowpea genome.