Recent radiations provide rare windows into the early stages of diversification. With the advent of second- and third-generation DNA sequencing technologies, it is now possible to study this process at the whole-genome level. However, few studies have taken a similarly comprehensive approach at the phenotypic level. This is what we do here, using the hamlets (Hypoplectrus spp.) as a model system. These reef fishes from the Greater Caribbean have diversified rapidly into 18+ species that differ essentially in terms of color pattern. Using a recently developed workflow, we analyzed \emph{in situ} photographs of 571 fishes from 14 species at pixel resolution with a fully standardized and automated procedure. The results show that sympatric species form phenotypic clusters that are significantly different from each other, but still exhibit substantial within-species variation and between-species overlap. At the scale of the Greater Caribbean, geographic variation within species further contributes to this overlap, resulting in nearly continuous variation across the entire radiation. A complementary dataset of 327 genomes from 18+ species indicates that similar patterns are observed at the population genomic level. These results demonstrate that sympatric clusters are maintained by selection on a phenotypic and genomic substrate that is largely continuous and shared across species.