AbstractIn this work, we have evaluated the host suitability of 29 pepper genotypes of Capsicum annuum and 9 of the related cultivated species C. chinense (4), C. frutescens (4) and C. pubescens (1) to Meloidogyne incognita in field conditions. The presence/absence of resistance genes in the pepper germplasm were also assessed using PCR‐specific markers linked to the N, Me1‐Mech2, Me3‐Me4 and Me7‐Mech1 genes. Intraspecific variability for M. incognita resistance was found. According to gall index (GI) and reproduction index (RI) the most resistant genotypes, which may contribute to nematode management, include three of C. frutescens (Fru‐2, Fru‐3 and Fru‐4) and seven of C. annuum (Ca‐3, Ca‐4, Ca‐5, Ca‐11, Ca‐15, Ca‐24 and Ca‐25). No egg masses or eggs were found in Fru‐3 and Fru‐4 genotypes as occurred in the resistant controls ‘SCM’, ‘CH’ and ‘Charlot’. The amplification of markers linked to resistance genes in genotypes with a suitable degree of resistance, together with the differences found between genotypes with regard to the gene and/or number of amplified markers, make this germplasm a valuable tool for further characterisation and pepper breeding.