Anemonefishes present scientists with a wealth of fascinating biological traits such as their natural symbiosis with sea anemones, sex change, dominance hierarchy, socially controlled growth rate, and conserved skin pattern development. Combined with their ease of upkeep and culturing in captivity, this has led to their emergence as a model group for studying ecology, evolution, and developmental biology in a reef fish. To identify the genes underlying a given trait and examine its molecular evolution, it is often necessary to conduct an initial general screening using forward genetic approaches (i.e., seeking the genetic basis of a phenotype or trait) or exploratory analyses of transcriptomes and/or genomes. This can then inform reverse genetic studies (i.e., seeking what phenotypes are controlled by specific genetic sequences) by performing more targeted in-vivo manipulations of genetic sequences. In this chapter, an overview is first given of the discoveries made by comparative genomic and transcriptomic studies on anemonefishes. Next, the potential usefulness of forward genetic approaches already applied in more established teleost models is discussed. Finally, an in-depth explanation is given on the application of the CRISPR/Cas9 genome-editing system in the false clown anemonefish (Amphiprion ocellaris), including current injection protocols for gene knockouts, notes on possible modifications for alternative edits (e.g., gene knock-ins), and the challenges to be addressed before achieving a reliable production of mutant anemonefish.