The Drosophila segment-polarity gene patched (ptc) is an integral component of the segmentation gene cascade acting in the early embryo. At later stages of embryogenesis, ptc is expressed in the primordia of epithelial placodes of a specific portion of the brain, the optic lobes. Mutant analysis shows that the lack of ptc activity alters the fate of optic-lobe primordia precursors. In ptc mutants they give rise to supernumerary neurons in the larval light-sensory system, termed Bolwig organ, which is derived from precursor cells next to the optic-lobe anlagen. We specifically eliminated ptc protein by chromophore-assisted laser inactivation (CALI) in late wild-type embryos. Such embryos show a normal segment pattern, but they develop phenocopies equivalent to the phenotype of ptc mutant Bolwig organs. Our results demonstrate that the CALI technique can be applied to separate genetic functions at different developmental stages of a living organism and that the segment-polarity gene ptc is redeployed to functionally discriminate between distinct developmental pathways in adjacent pools of precursor cells.