This paper presents high-density molecular linkage maps for the tomato and potato genomes, containing over 1000 markers with an average spacing of approximately 1.2 cM (about 900 kb). These maps were constructed using a common set of probes, allowing precise identification of breakpoints corresponding to five chromosomal inversions that differentiate the two species. All inversions appear to result from single breakpoints near or at the centromeres of affected chromosomes, leading to the inversion of entire chromosome arms. Recombination rates are uniformly distributed across chromosomes, but there is significant heterogeneity within chromosomes. Centromeric and centromeric heterochromatin regions experience up to 10-fold less recombination than other areas. About 28% of mapped loci are in regions of suppressed recombination, including both random genomic clones and transcribed genes. High-density maps have practical and evolutionary implications, facilitating chromosome walking, quantitative trait mapping, marker-assisted breeding, and evolutionary studies in these important crop species. The maps were constructed using RFLP and other molecular markers, with additional morphological and isozyme markers for orientation. The tomato map covers 1276 map units, with markers distributed unevenly across chromosomes. The potato map covers 684 cM, with five chromosomal inversions identified. The results suggest that chromosomal inversions in tomato and potato involve entire chromosome arms and single breakpoints near the centromere. The availability of high-density maps should facilitate studies on the genetic basis of quantitative traits and chromosome walking to economically important genes. The research was supported by grants from the National Research Initiative Competitive Grants Program and the Binational Agricultural Research and Development Fund.This paper presents high-density molecular linkage maps for the tomato and potato genomes, containing over 1000 markers with an average spacing of approximately 1.2 cM (about 900 kb). These maps were constructed using a common set of probes, allowing precise identification of breakpoints corresponding to five chromosomal inversions that differentiate the two species. All inversions appear to result from single breakpoints near or at the centromeres of affected chromosomes, leading to the inversion of entire chromosome arms. Recombination rates are uniformly distributed across chromosomes, but there is significant heterogeneity within chromosomes. Centromeric and centromeric heterochromatin regions experience up to 10-fold less recombination than other areas. About 28% of mapped loci are in regions of suppressed recombination, including both random genomic clones and transcribed genes. High-density maps have practical and evolutionary implications, facilitating chromosome walking, quantitative trait mapping, marker-assisted breeding, and evolutionary studies in these important crop species. The maps were constructed using RFLP and other molecular markers, with additional morphological and isozyme markers for orientation. The tomato map covers 1276 map units, with markers distributed unevenly across chromosomes. The potato map covers 684 cM, with five chromosomal inversions identified. The results suggest that chromosomal inversions in tomato and potato involve entire chromosome arms and single breakpoints near the centromere. The availability of high-density maps should facilitate studies on the genetic basis of quantitative traits and chromosome walking to economically important genes. The research was supported by grants from the National Research Initiative Competitive Grants Program and the Binational Agricultural Research and Development Fund.