We describe a method for making targeted double-strand breaks in Drosophila melanogaster using zinc finger nucleases (ZFNs). After design and construction of the appropriate coding sequences, synthetic mRNAs for the ZFNs are injected directly into fly embryos. Frequencies of target cleavage and mutagenesis in the range of 1-10% have been achieved at several different loci. A donor DNA carrying desired sequence changes can be incorporated in the injection mix and leads to targeted gene replacement, with particularly good efficiency when the recipient embryos are defective for nonhomologous end joining.