Physically linked clusters of genes that encode the enzymatic information for the synthesis of specialized metabolites are a well-established feature of microbial secondary metabolism. In contrast, the biosynthesis of plant specialized metabolites has until recently been thought to be almost exclusively encoded by genes that are randomly scattered in the genome. However, recent reports highlight the growing number of examples of gene clusters for specialized metabolic pathways in plants. Numerous gene clusters that encode for the biosynthesis of different classes of metabolite have now been discovered in a variety of plant species. Comparison of these characterized clusters now enables us to begin to define their salient features and to exploit plant biosynthetic gene clusters for synthetic biology applications.