Homologies of tomato and pepper genes have been compared, and genetic linkage maps have been constructed based on a common set of cDNA clones and selected single-copy genomic clones. We report here that the gene repertoire of these two species is highly conserved, yet the linear order of the genes on the chromosomes has been greatly modified. Although the two species share the same number of centromeres, the chromosomal regions around those centromeres have undergone extensive rearrangements. Accompanying the extensive chromosome rearrangement has been a change in locus number for approximately 12% of the loci detected by random cDNA clones. Duplicated loci within each genome are normally found on different chromosomes and are not confined to one species, thus ruling out gene duplication as an explanation for the 4-fold higher DNA content of pepper. At least one of the duplications occurred since the divergence of tomato and pepper from their last common ancestor.