In eukaryotes the arrangement of genes along the chromosome is not as random as it at first appeared, and distinctive clusters of functionally related but non-homologous genes can be found in the genomes of certain animals and fungi. These include the major histocompatibility complex in mammals and gene clusters for nutrient use and secondary metabolite production in fungi. A growing number of functional gene clusters for different types of secondary metabolite are now being discovered in plant genomes. However, the molecular mechanisms and evolutionary pressures behind their formation are poorly understood. Here we discuss the implications of our recent investigation into the origin of two functional gene clusters in the model plant Arabidopsis thaliana.