Potato virus X (PVX) resistance in potato is one of the best-characterized resistance models, however little is known in pepper. To evaluate the resistance to PVX in Capsicum annuum, a total of eleven pepper accessions were used for resistance screening against two PVX strains, USA and UK3. None of them were resistant against strain UK3, whereas four resistant genotypes were found against strain USA, three of which were further characterized. Two unlinked dominant genes were identified for both genotypes Bukang and Perennial; resistance in the genotype CV3 seemed to be conferred by two complementary dominant genes. These results demonstrated that the resistance to PVX in C. annuum is different from that in potato. This is the first report on genetic analysis of PVX resistance in C. annuum.