Mosaic analysis is used to assess gene function and cell autonomy in a subset of cells in an organism, and has been extensively applied in Drosophila studies. However, it is difficult to generate mosaic cells in Drosophila embryonic tissues using existing methods. Therefore, we developed a new method for generating genetic mosaic embryos using a modified Cre/loxP system. In this report, we also characterized the capabilities and limitations of this novel method.We first constructed a novel cassette combining loxP with the Actin 5C enhancer and Gal4 cDNA, and generated a transgenic fly carrying this construct (Aloxg-Gal4). In Aloxg-Gal4, the activation of Gal4 expression is suppressed by the gypsy insulator. Once the gypsy insulator is removed, however, Gal4 is expressed when site-specific recombination between loxP sites is induced by Cre recombinase. This system allowed the mosaic expression of Gal4 in Drosophila embryonic tissues (epidermis, amnioserosa, tracheal system, malpighian tubules, foregut, hindgut, midgut, and neuron), leading to the Gal4-dependent activation of arbitrary genes under the control of the upstream activation sequence (UAS).This practical method can be used to generate mosaic cells in Drosophila embryonic tissues and can be applied to any gene without specialized equipment.