Like all biological disciplines, phytochemical research has seen profound changes in recent years. Whilst enzyme and metabolite purification and characterisation and pathway identification remain vastly important, the relative ease at which we can now obtain genome scale information has facilitated analysis at the level of the metabolic network. In addition, in recent years we have experienced an explosion in the number of plant proteins for which structural information is available. However, despite the presence of sequence information from a growing number of photosynthetic species, the function of many genes, let alone their in vivo roles, remains unclear. This review attempts to provide both an overview of the current state of the art and a perspective of the major challenges that remain.