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One obstacle of the chili-s resistance breeding program to anthracnose disease is to find source of resistant gene. In addition, information of inheritance mode and genetic control has not yet been obtained accurately. Line AVPP0207 is a chili genotype that has an resistance gene from accession C chinense (PBC932) transferred into C. annum (IR * 3). Researcher in IVEGRI had succeeded to cross breeding genotype Tanjung-2 with line AVPP0207. The objectives of the study are: (1) to molecularly identify of pathogen isolates Colletotrichum spp from the field ; (2) to individually select of F2 generation that resistance to anthracnose, so that the inheritance mode can be identified. The study was conducted at Indonesian Vegetables Research Institute (IVEGRI) from January to December 2015. The use of specific primers Calnt2 / ITS4 showed a DNA band 490 bp in pathogen isolate 1, while the use of Cclnt / ITS4 showed a DNA band 460 bp in pathogen isolate 2. A total of 15 individually F2 plant numbers (7.07%) were successfully selected as resistant genotypes based on formed lessio diameter on the skin surface fruit (<4 mm). Inheritance mode of F2 chili generation (Tanjung-2 x AVPP0207) for resistance to isolate C. acutatum showed that resistant trait is recessive with incomplete gene action, there is no maternal effect, resistant gene is a major gene with an estimated number is 1.68, and broad-sense heritability (h2bs) is high (0.75).