The present invention relates to engineering new biosynthetic pathways into microorganisms, in particular biosynthetic carotenoid pathways. New and improved catalytic functions of metabolic pathways are created by, for example, site-specific mutation or gene shuffling techniques, to provide for efficient biosynthesis of carotenoids. By applying the described directed evolution techniques, almost any carotenoid could be produced, in a host cell, from one or a few sets of genes. In addition, the described techniques are useful for creating gene or protein libraries for new and uncharacterized carotenoids.