The gene Mi-1 confers effective resistance in tomato ( Lycopersicon esculentum) against root-knot nematodes and some isolates of potato aphid. This locus was introgressed from L. peruvianum into the corresponding region on chromosome 6 in tomato. In nematode-resistant tomato, Mi-1 and six homologs are grouped into two clusters separated by 300 kb. Analysis of BAC clones revealed that the Mi-1 locus from susceptible tomato carried the same number and distribution of Mi-1 homologs, as did the resistant locus. Molecular markers flanking the resistant and susceptible loci were in the same relative orientation, but markers between the two clusters were in an inverse orientation. The simplest explanation for these observations is that there is an inversion between the two clusters of homologs when comparing the Mi-1 loci from L. esculentum and L. peruvianum. Such an inversion may explain previous observations of severe recombination suppression in the region. Two Mi-1 homologs identified from the BAC library derived from susceptible tomato are not linked to the chromosome 6 locus, but map to chromosome 5 in regions known to contain resistance gene loci in other solanaceous species.