The question of how variation in the DNA translates into organismal diversity has puzzled biologists for decades. Despite of recent advances in evolutionary and developmental biology, the molecular mechanisms that underlie diversification, adaptation and evolutionary innovation remain largely unknown. The exceptionally diverse species flocks of cichlid fishes in the East African Great Lakes are textbook examples for adaptive radiations, and emerge as excellent model systems to study the genetic basis of biodiversity. East Africa’s hundreds of endemic cichlid species are akin a natural mutagenesis screen and differ greatly in ecologically relevant and, hence, naturally selected characters such as mouth morphology, but also in sexually selected traits such as coloration. Here, I propose to study the relative adaptive relevance and the molecular basis of characters that contributed to the origin of the cichlids’ astonishing species-richness, making the underlying genetic pathways prime targets in the quest of “speciation genes”. Specifically, I aim to focus on three unique characters of cichlids: (i) thick lips that evolved independently in different cichlid assemblages; (ii) the highly adaptable pharyngeal jaw apparatus; and (iii) egg-dummies on the anal fins of male haplochromines, which play an important role in the breeding cycle of these mouthbrooding fishes. A major goal of this project is to test whether the same developmental and genetic pathways are involved in the origin of evolutionary parallelisms in cichlid radiations. To this end, I will use microarray, RT-PCR and in situ hybridization experiments to compare thick-lipped species, parallel pharyngeal jaw morphologies and similar color patterns on fins of cichlids of different assemblages, as well as the egg-spots of haplochromines to those of unrelated ectodine cichlids, in which similar dummies have evolved independently and on a different fin. Finally, I intend to compare the genes underlying these characters in an evolutionary genomic framework in order to evaluate the relative strength and the type of selection that has acted on loci involved in the morphogenesis of naturally versus sexually selected traits in cichlid adaptive radiations.