Abstract: A total of sixty Colletotrichum isolates were purified from anthracnose disease samples, collected from 15 chilli growing districts of Karnataka. The isolates were evaluated for their morphological and genetic characterization using AFLP marker assay. Based on the morphological characterization, 40 isolates were identified as Colletotrichum capsici/truncatumand 20 as C. gloeosporioides. Considerable morphological variability was observed in C. gloeosporioides isolates compared to C. capsici isolates. AFLP marker assay could clearly differentiate the C. capsici and C. gloeosporioides isolates at 43% genetic similarity, thus complementing species classification based on morphological characterization. However, morphological and AFLP grouping of isolates indicates no clear correlation between clustering in the dendrogram and morphological grouping of C. capsici and C. gloeosporioides isolates this suggested existence of wide variability in both the species.