Indigo is a widely used dye in the textile industry, but current industry practice uses toxic chemicals to produce and solubilize the compound. I am developing a more environmentally friendly dye process by using microbial fermentation to produce indigo dye. Unlike the industrial procedure, microbes can produce indigo from renewable sources, and many of the hazardous chemicals can be eliminated from the dye synthesis and dye application processes. First, I describe a method to dye with indican, the glucosylated form of an unstable indigo precursor found in indigo-producing plants. I identified the gene sequence for a key biosynthetic enzyme from the indigo plant, and I expressed that gene in an Escherichia coli strain to produce indican. The glucosyl group on indican can be removed by a β-glucosidase, forming indigo. I show that applying indican and β-glucosidase to cotton can dye it an indigo color. Second, I extend this strategy of biological protecting groups towards producing a second-generation dye molecule, isatan B. Although chemically similar to indican, isatan B is hydrolyzed at a basic pH, a desirable property for the indigo dyeing process. I isolated the isatan B molecule from plant leaves and used the purified molecule to characterize isatan B’s stability in the E. coli host. I then describe efforts to construct a biosynthetic pathway for isatan B in E. coli.