Anthracnose (Colletotrichum spp.) causes significant yield losses in chili pepper (Capsicum annuum L.), and several loci conferring resistance to this disease have been identified. Seven and one amplified fragment length polymorphic (AFLP) markers were additionally located on LG 12 (CaR12.2, major locus resistant to Colletotrichum acutatum) and LG 9 (CcR9, major locus resistant to C. capsici), respectively, through AFLP analysis combined with extreme bulked segregant analysis (BSA). Among these, two AFLP markers, EtagMcgt04 (CaR12.2) and EtacMccg13 (CcR9), were converted into sequence tagged site (STS) markers (CaR12.2M1-CAPS and CcR9M1-SCAR, respectively), via sequencing analysis of internal and flanking regions of each AFLP marker. The selection efficiencies were 72% for CaR12.2M1-CAPS and 82.5% for CcR9M1-SCAR. These simple PCR-based markers will be useful for breeding cultivars with enhanced resistance to anthracnose, for pyramiding resistances to both C. acutatum and C. capsici, and for further characterization of the locus, including isolation of genes responsible for resistance.