Marked clones in mosaic animals have been used extensively to answer developmental questions in Drosophila. Recently, the use of the FLP/FRT system has allowed for the high-frequency production of mosaic animals for 95% of Drosophila genes. Cell markers have been engineered in this system to label mutant clones in both developing tissues and adult cuticle. Strains carrying these genetically marked FLP/FRT chromosomes have greatly enhanced our ability to study gene function in both germline and somatic Drosophila cells.