Pepper (Capsicum annuum L.) belongs to family Solanaceae. It is an agronomically important plant originating from Mexico. Pepper yield, quality and growth are limited by plant nematode parasitism. Root-knot nematodes (Meloidogyne spp.) are the most damaging sedentary endoparasites. M. incognita race 2 is the most common root-knot nematode found in Turkey. The Me1 gene which confers resistance to M. incognita was mapped in pepper to a 28 cM interval on chromosome 9. The aim of this study was to develop molecular markers linked to this nematode resistance gene. Phenotypic characterization of nematode resistance was performed for 200 F2 individuals from the cross between resistant pepper cultivar PM217 and Turkish susceptible cultivar AZN-1. In the F2 individuals, 151 plants (76%) were evaluated as resistant, 49 plants (24%) were susceptible. Markers were tested on parents of the mapping population to identify polymorphisms. A total of 30 standard markers and 548 new marker combinations were tested. Of these 578 markers, 75 (13%) were polymorphic. They were applied to F2 population and 28 (37%) showed clear segregation on F2 population. Eighteen of the markers (64%) segregated dominantly, 10 of the markers (36%) segregated codominantly. Markers located near Me1 on chromosome 9 were used for the construction of a linkage map. Out of three markers, SCAR_CD was the nearest marker to Me1 gene with a distance of 1.1 cM. These markers will provide selection at the genotypic level by marker-assisted selection, which will increase the efficiency and effectiveness of pepper breeding for nematode resistance.