The question of how genetic variation translates into organismal diversity has puzzled biologists for decades. In spite of recent advances in evolutionary and developmental biology, the molecular mechanisms that underlie diversification, adaptation and evolutionary innovation remain largely unknown. It has become more and more clear, though, that only a limited genetic “toolkit” exists and that the evolution of morphological diversity is to a large extend driven by novel interactions between an existing set of genes. What is still less clear is the nature of changes in the genome that ultimately are responsible for the origin of morphological diversity and how genetic, transcriptional, morphological and ecological diversity are interrelated. The exceptionally diverse species-flocks of cichlid fishes in the Great Lakes of East Africa are an excellent model system to study biological diversification. Lakes Tanganyika, Malawi and Victoria are each teeming with a unique set of hundreds of endemic cichlid species that evolved in the last few millions to several thousands of years only. East Africa’s hundreds of closely related cichlid species are akin a natural mutagenic screen and differ greatly in ecologically relevant and, hence, naturally selected characters, such as the mouth apparatus, as well as in sexually selected traits, such as coloration. This suggests that both ecological and non-ecological factors might be modulating diversification in cichlid species-flocks. One of the most astounding aspects of cichlid evolution is the frequent occurrence of evolutionary parallelisms. This has led to the question whether natural selection alone is sufficient to produce parallel forms, or whether a developmental or genetic bias has influenced the direction of diversification in cichlids. Here, I propose an integrative approach towards the understanding of animal diversification in general, and of explosive speciation and adaptive radiation in cichlids in particular. Taking advantage of the unparalleled eco-morphological richness of cichlids and the replicative nature of their adaptive radiations, I plan to focus on the interrelationship between genetic, transcriptional, phenotypic and ecological diversity in natural populations. To this end, I intend to combine a large-scale population-genomic study on the basis of newly designed single nucleotide polymorphism (SNP) markers and DNA sequence fragments of ca. 30 nuclear loci with comparative gene expression assays and eco-morphological assessments in the same set of populations. Forty populations representing the cichlids’ phylogenetic diversity in East Africa will be sampled and subjected to population-genomic analysis. For the gene expression assays, I intend to establish two new reference transcriptomes for Lake Tanganyikan cichlids to then perform a genome-wide analysis of gene expression in relevant tissues using novel sequencing technologies. Variation in gene expression in selected natural populations can then be analyzed by quantitative real-time PCR. Geometric morphometric techniques (which allow the quantification of morphological variation) and stomach content and stable-isotope based nutrition analyses (which are good estimators for ecological diversity) will serve as proxy for niche dimensionality. It will thus be possible to determine the relative contribution of genetic versus transcriptional diversity to morphological and ecological variation in descendents of cichlid adaptive radiations. In addition, we will evaluate whether the observed genetic and transcriptional diversity is evenly distributed across the cichlids’ genome or whether certain hotspots exist, which could be responsible for the cichlids’ propensity for explosive speciation. The massive amount of comparative population-genomic data in combination with our sampling design will furthermore allow us to focus on the evolution of parallel morphologies. We will so be in the position to address the eminent question whether the same genes or genetic pathways are involved in the morphogenesis of parallel traits. A final goal of this project is to determine the relative importance of ecological and non-ecological factors in cichlid adaptive radiations. With all these data in hand, I expect exciting new insights into the process of organismal diversification in general and into one of evolutionary biology’s best model systems, the adaptive radiations of cichlid fishes, in particular.