In pepper (Capsicum annuum L.), the resistance genes Me1 and Me3 have been shown to control the main species of root-knot nematodes, Meloidogyne spp. Here, the reactions to inoculation with Meloidogyne incognita second-stage juveniles (J2) of two resistant doubled haploid pepper lines, HDA149 and HDA330, obtained through in vitro androgenesis and carrying Me3 and Me1 respectively, were compared in time-course experiments. Although they both suppressed nematode reproduction, the two resistance genes induced very different response patterns. First, significantly fewer J2 were able to invade roots of HDA149 compared to HDA330. Second, while ultrastructural changes typical to the hypersensitive reaction (HR) occurred in root cells of HDA149 early after nematode inoculation (i.e. necrosis of cells directly involved in nematode penetration and feeding), the resistance mechanism in HDA330 involved a delayed plant response (i.e. cell senescence and death) which took place after the induction of a number of (imperfect) giant cells by the nematode. These differential responses are discussed in relation to the nematode ability to circumvent or not the resistance gene(s), and it is suggested that such virulence could result from the overcoming by the J2 of the early HR occurring within the epidermis and cortex of the root.