In this study, tomato and pepper populations were phenotypically and genotypically characterized to identify cucumber mosaic virus (CMV) resistant lines and determine the genetic control of resistance. Populations of both crops and their resistant and susceptible parents were mechanically inoculated with CMV. Plants were evaluated visually and by enzyme-linked immunosorbent assay (ELISA). Since virus was detected only in inoculated leaves but was not usually present in uninoculated leaves of symptomless plants, CMV resistance appeared to be true resistance not immunity. According to phenotypic analysis of F2 tomato population, it was hypothesized that two dominant genes were controlling resistance as the plants fit a 9:7 (resistant:susceptible) segregation ratio as determined by Chi square goodness-of-fit analysis. In order to perform quantitiative trait locus (QTL) analysis, molecular markers were surveyed for polymorphism using the two parents of the tomato population, L. esculentum and L. hirsutum LA1223. According to QTL analysis (using 107 polymorphic markers), 11 genomic regions were linked to CMV resistance. For seven loci, resistance alleles were coming from the L. hirsutum parent as expected. However, for four loci, resistance was associated with alleles from the CMV susceptible parent, L. esculentum. These results show that the genetic potential for resistance cannot be determined by only looking at the phenotype of the two parents. As a result of this work, developing elite lines or transferring resistance genes into cultivated species by marker assisted selection will be easier.