Root-knot nematodes (Meloidogyne spp.) resulted significant yield losses in peppers. It has been reported that at least 10 dominant genes (N, Me1, Me2, Me3, Me4, Me5, Me6, Me7, Mech1 and Mech2) associated with resistance to Meloidogyne spp. are thought to act independently in gene-for-gene interactions in pepper. Several molecular markers were developed for these genes to be used in marker-assisted selection (MAS). The markers include N-SCAR, SCAR_B94, SCAR_CD, SCAR_PM6a, SCAR_PM6b, and SCAR_PM54. In this study, the pepper genotypes reported to carry different resistant genes against the nematodes were artificially inoculated with root-knot nematode (Meloidogyne incognita race 2) and compared via the linked molecular markers. Of all the markers tested, the SCAR_PM54 marker results were fully consistent with artificial nematode testing, correctly predicting resistant and susceptible genotypes. The results documented once again that the linked markers should be confirmed through classical testing before utilizing them in MAS.