The tomato genome sequence, along with that of its wild relative *Solanum pimpinellifolium* and the potato genome, provides insights into the evolution of fleshy fruits. The domesticated tomato genome shows only 0.6% nucleotide divergence from *S. pimpinellifolium* and recent admixture, while diverging more than 8% from the potato genome. The tomato genome has experienced two major genome triplications, one ancient and shared with rosids, and a more recent one, which set the stage for neofunctionalization of genes controlling fruit characteristics. Comparative genomics reveals that the tomato genome is highly syntenic with other Solanaceae genomes and has fewer high-copy retrotransposons compared to Arabidopsis and Sorghum. The tomato genome is partitioned into three subgenomes based on alignments to the grape genome, suggesting a whole-genome triplication in the Solanum lineage. This triplication, followed by gene loss, contributed to the formation of major eudicot lineages. Fleshy fruits are important for seed dispersal, and the genome sequences provide a basis for understanding the evolution of fruit-specific functions, such as ethylene biosynthesis and red light perception. The tomato genome also allows systems approaches to fruit biology, including the study of gene families like the SELF PRUNING (SP) gene family, which controls flowering and fruit yield. The availability of the tomato and *S. pimpinellifolium* genomes will aid in biodiversity-based breeding and trait introgression from wild relatives.The tomato genome sequence, along with that of its wild relative *Solanum pimpinellifolium* and the potato genome, provides insights into the evolution of fleshy fruits. The domesticated tomato genome shows only 0.6% nucleotide divergence from *S. pimpinellifolium* and recent admixture, while diverging more than 8% from the potato genome. The tomato genome has experienced two major genome triplications, one ancient and shared with rosids, and a more recent one, which set the stage for neofunctionalization of genes controlling fruit characteristics. Comparative genomics reveals that the tomato genome is highly syntenic with other Solanaceae genomes and has fewer high-copy retrotransposons compared to Arabidopsis and Sorghum. The tomato genome is partitioned into three subgenomes based on alignments to the grape genome, suggesting a whole-genome triplication in the Solanum lineage. This triplication, followed by gene loss, contributed to the formation of major eudicot lineages. Fleshy fruits are important for seed dispersal, and the genome sequences provide a basis for understanding the evolution of fruit-specific functions, such as ethylene biosynthesis and red light perception. The tomato genome also allows systems approaches to fruit biology, including the study of gene families like the SELF PRUNING (SP) gene family, which controls flowering and fruit yield. The availability of the tomato and *S. pimpinellifolium* genomes will aid in biodiversity-based breeding and trait introgression from wild relatives.