<p>Pepper (<i>Capsicum annuum</i>) is one of the most important vegetables. Root-knot nematodes (RKNs) can severely damage peppers worldwide. The utilization of resistance (R) genes in peppers represents an economically viable and environmentally sound approach for the management of RKNs. In the management strategy, the choice of the R gene is crucial to suppressing nematode populations and the sustainability of these R genes as single or combinations. In this study, the performance of pepper cultivars with varying combinations of <i>Me1</i> and <i>N</i> genes which are homozygous and heterozygous, regarding resistance to <i>Meloidogyne incognita,</i> was investigated. Ten pepper cultivars were tested with <i>M. incognita</i> under the controlled conditions. As a result of the study, the response of pepper cultivars against <i>M. incognita</i> was found as resistant in all single or combinations of homozygous and heterozygous status of <i>Me1</i> and <i>N</i> genes. However, the level of the resistance was found significantly different, especially in both homozygous and heterozygous resistance genes (<i>Me1</i> and <i>N</i>) in pyramided cultivars. Molecular marker results supported the presence of both genes <i>Me1</i> and <i>N</i> genes with different statuses by homozygous and heterozygous positions in pepper cultivars. These results indicate that the choice of the resistance gene is important for the control and durability of the gene.</p>