Colours and associated patterns are probably some of the most obvious phenotypic traits in animals and reef teleost fishes are often cited as a textbook example for illustrating this type of diversity. Even if it is well established that colour patterns play a central role in the ecology and evolution of reef fishes, we still lack the necessary toolkits to fully grasp the mechanisms driving the diversification of this obvious phenotypic trait. On the one hand, genotyping power seems now limitless thanks to current DNA sequencing technologies. Today, entire genomes of fishes can be easily produced for large sets of species. On the other hand, the description of colour patterns and the quantification of their variation across reef fishes might be highly challenging. In a cover manuscript in this issue of Molecular Ecology, Coulmance et al. (2023) introduced an innovative approach for extracting and quantifying the major colour pattern elements present in the hamlets (Hypoplectrus spp., Serranidae), a recent reef fish radiation from the Caribbean. Then, they intelligently used the quantified colour pattern variation as a phenotypic trait for a genome-wide association study (GWAS). Interestingly, using a method that required no a priori knowledge, they were able to recover well-established marks (e.g., vertical bars) and to highlight less expected colour pattern elements (e.g., dark to light gradient on ventral part as well as caudal and anal fins), which show strong association peaks on linkage group (LG) 12 and 04. Beyond the demonstration of the potential of their new quantitative analysis of colour pattern variation in reef fishes combined with GWAS, their findings offer new perspectives on our understanding of the intrinsic and extrinsic factors generating this outstanding diversity of the fish world.