Use of zinc finger nucleases is an established method for gene targeting in zebrafish. Such strategies are efficient in targeting a single gene of interest. Our study attempts to target many Nodal related genes by targeting the Activin Response Element (ARE) through the use of native DNA binding domains tethered to the Fok1 endonuclease. In this light, genes are targeted in a Nodal-dependent manner, and can retain transcript levels sustained by other signaling pathways. This technique holds the potential to be a high throughput means of generating mutations in the regulatory regions of various Nodal responsive genes with the use of one set of constructs.