One advantage of the zebrafish model system is the ability to use forward genetics to reveal critical gene functions by their mutant phenotype. Reverse genetic tools are available, although it is more challenging and time-consuming to identify mutations in specific genes of interest and virtually impossible to induce mutations in a targeted manner. Two recent papers have shown that locus-specific zinc-finger nucleases (ZFNs) can be used to create mutations in investigator-specified loci at high frequency, generating considerable enthusiasm that the technology may be generally applicable to many zebrafish genes. The rate-limiting step in ZFN application is typically the zinc-finger protein (ZFP) design phase, partly because ZFPs that bind to intended target sequences in naked DNA may not recognize the target within chromatin, or may recognize cryptic sites. Importantly, both papers also provide new tools to validate or pre-select ZFNs that work well in vivo and thus greatly facilitate the identification of active ZFNs. Finally, work in other model systems and in cultured cells show that ZFNs can facilitate homology-directed repair, raising the exciting possibility that ZFNs may facilitate homologous recombination in zebrafish, allowing site-specific modification of endogenous genes via a method that does not require embryonic stem cell technology.