Genetic resistance to cucumber mosaic virus (CMV) in pepper (Capsicum spp.) is recessive, polygenic and, therefore, has been difficult to transfer in breeding programs. Although a few varieties have been released with some resistance, in our tests, these develop severe symptoms that are eventually indistinguishable from the susceptible reactions. Furthermore, accurate and consistent screens for the disease can be relatively difficult; therefore, we report on the detection molecular markers linked to two CMV resistance genes using distributional extreme analysis to identify the relevant quantitative trait loci (QTL). The 12 most resistant and 15 most susceptible individuals were selected from a segregating F2 population of 316 individuals that were derived from the interspecific cross (C. annuum `Jupiter' × C. frutescens BG2814-6). A total of 132 tomato genomic, cDNA, and pepper genomic clones were hybridized to filters with DNA extracted from the distributional extremes. These clones included framework markers representing all pepper linkage groups and also selected clones from regions of the genome identified in a preliminary analysis as possibly involved with CMV resistance. Several clones from the two regions of the genome previously identified appear to be nonrandomly cosegregating with the CMV resistance phenotype in this larger population. Further analysis will be done by adding more markers in the regions and refining the positions of the resistance QTL.