Brown blotch disease, caused by Colletotrichum capsici, is an important disease of cowpea with a significant yield losses ranging from 42 to 100% in West Africa. In this study, a specific polymerase chain reaction (PCR) primer set CC1F1/CcapR was used to characterize and to study the phylogenetic relationship of thirty eight strains of Colletotrichum species. This primer set is capable of amplifying only C. capsici from different fungal structures and provide a powerful tool for C. capsici detection in brown blotch disease in cowpea. Phylogenetic analysis from neighbor-joining (NJ) showed a high genetic variability in the rDNA-ITS region of the isolates. The isolates formed four groups or clusters on the basis of specific fragment analysis. Groups I, II, and III consist of strains containing specific region length of twenty one nucleotides and were considered as variant 1 of C. capsici. Group IV was a heterogeneous and consists of variants 1, 2, 3, and 4 of C. capsici. Key words: Cultivars, internal transcribed spacer (ITS) sequence, Colletotrichum species.
