jats:p Identifying genetic loci underlying trait variation provides insights into the mechanisms of diversification, but demonstrating causality and characterizing the role of genetic loci requires testing candidate gene function, often in non-model species. Here we establish CRISPR/Cas9 editing in jats:italicAstatotilapia calliptera</jats:italic> , a generalist cichlid of the remarkably diverse Lake Malawi radiation. By targeting the gene jats:italicoca2</jats:italic> required for melanin synthesis in other vertebrate species, we show efficient editing and germline transmission. Gene edits include indels in the coding region, probably a result of non-homologous end joining, and a large deletion in the 3′ untranslated region due to homology-directed repair. We find that jats:italicoca2</jats:italic> knock-out jats:italicA. calliptera</jats:italic> lack melanin, which may be useful for developmental imaging in embryos and studying colour pattern formation in adults. As jats:italicA. calliptera</jats:italic> resembles the presumed generalist ancestor of the Lake Malawi cichlids radiation, establishing genome editing in this species will facilitate investigating speciation, adaptation and trait diversification in this textbook radiation. </jats:p>