The shape, size and properties of any organism—animal, plant or microbe—are determined by the information encoded in its genome (DNA) and how the readout of this information is modulated by its interactions with the environment. The last decade has provided numerous examples of how genomic information has guided and informed our understanding of human, animal and plant health and disease. However, because of the costs involved, application of genomic approaches was previously limited to humans and the major agricultural plants and animals. Within the last few years, the development of new DNA sequencing technologies has revolutionized the study of crop plants. New technologies are now available that provide high-throughput DNA sequence coverage at low cost, making their application to smaller crops possible. Two research groups are currently applying these new technologies to Vanilla planifolia to study some of the important issues with Vanilla, such as disease susceptibility and vanillin biosynthesis.