Two SNP maps were constructed from two Chili populations including Capsicum annuum x C. chinense ‘PBC932', and C. baccatum ‘PBC80' x ‘CA1316', aiming to identify QTLs for anthracnose resistance. The ‘PBC932'-derived map contained 12 linkage groups (LG) with 214 SNPs and 824 cM coverage. The ‘PBC80'-derived map contained 12 LGs with 403 SNPs and 1,270 cM coverage. Based on the ‘PBC932' map, two QTLs corresponding to the anthracnose resistances in mature green and ripe fruit stages were identified on the same location of LG2 between two SNPs within 14 cM. Based on the ‘PBC80' map, three QTLs were identified in the ripe fruit stage, which corresponded to different resistance traits that were assayed by different inoculation methods (microinjection or MI and high pressure spray or HP) with two different pathotypes (PCa2 and PCa3). All the three major QTLs for the resistance traits assayed by PCa2/MI, PCa3/MI, and PCa3/HP were located on LG4 between two SNP markers within 17 cM.