Crocin and picrocrocin are the main components of the saffron. Both compounds are glucosylated and are responsible for the taste, colour and flavour of the spice. In addition, other apocarotenoids present in saffron could also be responsible for the organoleptic properties of the spice. Understanding factors regulating biosynthesis of these compounds and roles they play in the physiology and development of plants is critical. Three clones encoding dioxygenases enzymes have been isolated in our laboratory. The isolation and characterization of the genes implicated in the biosynthetic pathway of the saffron secondary metabolites, the compartmentalization of enzymes and substrates, is the key to understanding potential outcomes of altering these factors during production of transgenic plants or microorganism and evaluating physiological responses to “upstream” and “downstream” regulation of metabolic pathways.