Lake Victoria has one of the highest endemic fish species-area-relationships of any freshwater bodies in the world. More than 90% of this diversity is composed of haplochromine cichlids that have undergone an evolutionary radiation in the region into more than 700 endemic species in the past 100,000 years. These species belong to more than 20 different major ecological guilds from large benthic and small pelagic herbivores at one end of the consumer food web to inshore and pelagic fish predators at the other end. This diversity is rapidly being lost to eutrophication, invasion of other species and other environmental change, with repercussions for the ecosystem. Ironically, the diversity of these fish has been frustrating their conservation. Hundreds of species have to be distinguished, many of which are taxonomically still undescribed, and simple genetic techniques such as DNA barcoding cannot distinguish the species because of their relatively recent evolutionary origins. This has often led to situations where biodiversity management focuses on all the other non-endemic and less diverse taxa but falls short of documenting and monitoring the globally unique and strongly threatened regional heritage of haplochromine cichlids. Over the past years scientists have done extensive sampling and genome sequencing of hundreds of haplochromine species from all major and some minor lakes in the region. They find strong genome-wide differentiation between species, between genera and between ecological guilds of cichlids that was unexpected given the recency of the radiation and the failure of bar coding and mitochondrial DNA sequencing in general. This research project reconciles these observations through a reconstruction of the evolutionary history of the cichlid radiations of the Lake Victoria region. It will then use the data to present an integrated picture of the historical, biogeographical and ecological structure of this global biodiversity hotspot and make recommendations for steps towards an integrated conservation assessment.