A general, non‐invasive method to trace morphogenesis in living Drosophila was developed. To label specific cells, green fluorescence protein (GFP) of jellyfish Aequorea victoria was expressed by the Ga14‐UAS system. Green‐fluorescence from GFP fused to the nuclear localization signal was detectable in polytene larval tissue, but not in diploid tissue. Further fusion to bacterial β‐galactosidase produced GFPN‐lacZ, which fluoresced brightly in several diploid larval and embryonic tissues. GFPN‐lacZ was used to trace dynamic cell movement during the formation of the embryonic tracheal system. These results indicate that GFPN‐lacZ can be used to mark specific cells to study cell movement and gene expression in living animals.