We report a new technique using fluorescent probes to detect a mRNA and a protein simultaneously in the Drasophila embryo. For in situ hybridization, 3-hydroxy-N-2'-biphenyl-2-naphthalenecarboxamide phosphate ester (HNPP)/Fast Red TR was used as a fluorescent substrate for alkaline phosphatase. It was possible to compare protein and mRNA expression on a cell by cell basis with a laser scanning confocal microscope. We applied this technique to analyse the dynamics of Distal-less (Dll) enhancer activity in the thoracic limb primordium in the early Drosophila embryo. We stained embryos bearing the Dll early enhancer (Dll-304) fused to the Escherichia coli lacZ gene. LacZ mRNA was delectable in the ventral region of the limb primordium, and beta-galactosidase protein in the dorsal region. In the middle, both mRNA and protein were detectable. These results suggest that the Dll enhancer is activated in the ventral region of the Limb primordium and that Dll-positive cells migrate from a ventral position to a dorsal one within a single limb primordium.