Technical Abstract: Limited genetic variation has been observed within tomato (Solanum lycopersicum L.), although no studies have extensively surveyed single nucleotide polymorphism (SNP) diversity among tomato landraces. We estimated intraspecific DNA sequence variation by analyzing 50 gene fragments (22.9 kb) per plant in a 31 plant diversity panel, and uncovered evidence of natural interspecific hybridization as well as human-aided introgression. Three populations - primary centers of diversity, contiguous countries, and secondary centers, were not genetically differentiated (FST = 0.03). Mean expected heterozygosity decreased (He = 0.254, 0.152, 0.092, respectively) while mean coefficient of inbreeding increased (FIS = 0.793, 0.947, 1.000, respectively), in the populations. The majority of loci (80%) were polymorphic with the minor allele at a frequency of 10% or less for most (141 of 155) SNPs. Mean diversity as estimated by theta and pi was approximately 1.5 SNPs per kb. Significant linkage disequilibrium was observed between 19% of locus pairs, and within-locus population recombination estimates were negligible. We also sequenced 43 gene fragments from wild tomato Solanum arcanum Peralta as an outgroup. Various statistical tests rejected a neutral equilibrium model of molecular evolution at 10 of 50 loci. Interspecific introgression was inferred for at least seven tomato lines and five loci. Introgressed alleles likely originated both from natural hybridization with Solanum pimpinellifolium and from crosses with wild relatives for crop improvement. Extensive introgression and frequent bottlenecks within S. lycopersicum pose a challenge to reconstructing the genetic bases of domestication and selection using methods that rely on patterns of molecular polymorphism.