Zebrafish (Danio rerio) is a unique model organism at the functional intersection between a high fecundity and conserved vertebrate physiology while being amenable to a multitude of genome editing techniques. The genome engineering field has experienced an unprecedented rate of growth in the recent years since the introduction of designer endonucleases, such as zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats–Cas9 systems. With the ever-evolving toolset available to the scientific community, the important question one should ask is not simply how to make a mutant line, but rather how best to do so. For this purpose, understanding the toolset is just one end of the equation; understanding how DNA is repaired once double-strand breaks are induced by designer endonucleases, as well as understanding proper fish handling and line maintenance techniques, are also essential to rapidly edit the zebrafish genome. This chapter is outlined to provide a bird's-eye view on each of these three components. The goal of this chapter is to facilitate the adoption of the zebrafish as a model to study human genetic disease and to rapidly analyze the function of the vertebrate genome.