The inheritance of the root–knot nematode, Meloidogyne incogenita Race 2, resistance in the crosses segregation ratio in pepper cultivars, capsicum annuum, suggested a single dominant gene for the high level of resistant. Although the data on disease expression were recorded on 1 to 5 scale gall index, the results and subsequent observation fitted a single gene model for resistance better than a quantitative pattern. In general, the overall results for evaluation of pepper F1 progeny reaction to the root knot nematode using specific ISSR markers showed that, both crosses (P7xP5) and (P7xP4) exhibited five specific marker bands for highly resistance to root knot nematode. One of these specific marker bands with molecular size 860 bp, in (P7xP5), did not appear in either resistant or susceptible parents. In addition, the cross (P7xp3) gave only one specific marker band with molecular size 344 bp for resistance to root knot nematode.