Coral reefs are one of the most diverse ecosystems found on Earth, even though they only comprise a small fraction of the ocean. Marine fish species found on coral reefs display a wide variety of colours and patterns. Most of the reef fishes we recognise today are geologically recent, and their main ecological functions were developed around 20 Ma. From the late Miocene onward, many common reef fish lineages were still diversifying, although the sole innovation appears variations in their colour patterns. Research has shown that some related species that coexist in sympatry tend to be more different to one another than those that are allopatric. I examined the prediction that bigger differences in colour patterns would be detected in phylogenetically related reef fishes living in sympatry compared to those that live in allopatry. I selected seven clades, comprising 36 species, from four families of characteristic reef fishes (Grammatidae, Pomacanthidae, Lutjanidae and Labridae). Clades were selected based on whether or not they had both sympatric and allopatric species. Images of each species were compiled and measured differences in colouration and pattern using image analysis software. Colordistance and Patternize scores were significantly higher in sympatric species than in allopatric species for all but one of the studied clades, indicating higher dissimilarity in colour patterns within the same clade. As expected, the level of species relatedness affects colour divergence in reef fishes, likely because of phylogenetic conservatism. However, even among sister-species, there appears to be a larger dissimilarity in colouration when they coexist in sympatry. Colour divergence among sympatric species may have originated to facilitate better species recognition, which reduces aggression and helps locate a mate but also prevents hybridisation of closely related sister-species.