Tomato is an important agronomic crop and is a model system for the Solanaceae. To improve breeding programs and gain a better understanding of gene and genome function, identifying diversity present in wild species is crucial. Towards this end, we have sequenced the genome of Solanum galapagense, a perennial wild tomato species indigenous to the Galapagos Islands. The objective is to identify the genomic differences that may relate to the divergent phenotype of this wild species, which has evolved in relative isolation. Of particular interest are its high salt tolerance, differences in resistance to pathogens, as well as morphological variation. The genome was sequenced using the Illumina HiSeq paired-end approach to obtain about 30X coverage. The resulting genome assembly will be compared to the tomato reference sequence, to identify SNPs that will be used to study patterns of selection across the genome. Structural variation, such as gene duplications and inversions will be analyzed. Additionally, de novo assembly of the reads will allow for the detection of novel large indels that are present in this genome. All data will be publicly available at the Sol Genomics Network site (http://solgenomics.net/).