Kim et al. (2008c) used the BAC clones to develop markers linked to quantitative trait loci (QTLs) controlling resistance to Phytopthora capsisi. To fi nd these markers, a molecular linkage map was constructed using 100 F2 progenies of a cross between C. annuum, CM334 (resistant) and C. annuum, Chilsungcho (susceptible). The map, which consisted of 209 molecular markers, was used to detect four QTLs explaining 66.3 percent of the total phenotypic variation for root rot resistance and three QTLs explaining 44.9 percent of the total phenotypic variation for damping-off resistance. BAC clones were screened for two of these QTLs and were used to develop single-nucleotide amplifi ed polymorphism markers and cleaved amplifi ed polymorphic sequence markers, which can be used to screen for the Phytopthora capsisi resistance phenotype.