Adaptive radiation is the likely source of much of the ecological and morphological diversity of life. How adaptive radiations proceed and what determines their extent remains elusive in most cases. Here we report the in-depth examination of the spectacular adaptive radiation of cichlid fishes in African Lake Tanganyika. Based on whole-genome phylogenetic analyses, multivariate morphological measurements of three ecologically relevant trait complexes (body shape, upper oral jaw morphology, and lower pharyngeal jaw shape), scoring of pigmentation patterns, and approximations of the ecology of virtually all ~240 cichlid species endemic to Lake Tanganyika, we show that the radiation occurred within the confines of the lake and that morphological diversification proceeded in consecutive trait-specific pulses of morphospace expansion. We provide empirical support for two theoretical predictions on how adaptive radiations proceed, the ‘early-burst’ scenario (for body shape) and the stages model (for all traits investigated). Through the analysis of two genomes per species and by taking advantage of the uneven distribution of species in subclades of the radiation, we further show that species richness scales positively with per individual heterozygosity, but is not correlated with transposable element content, number of gene duplications, or genome-wide levels of selection in coding sequences.