Understand the forces generating biodiversity as well as the threats to losing diversity is critical for its conservation. Alpine whitefish are a lineage that have diversified particularly fast and are especially species rich in Swiss lakes. Alpine whitefish are further economically highly relevant for fisheries in Switzerland and their endemic diversity is impacted by management practices and anthropogenic changes to their habitat. As reproductive isolation between Alpine whitefish species is mediated by the environment, environmental change can weaken reproductive isolation and result in extinction through hybridization. By this process called speciation reversal, extinct species can transfer traces of their genomes into their sister species through introgressive hybridization. Using historical and contemporary samples, we sequenced whole genomes of all four species of an Alpine whitefish radiation before and after anthropogenic lake eutrophication and of one species through speciation reversal. Despite the associated loss of the profundal taxon, a substantial proportion of its genome, including regions shaped by positive selection before eutrophication, persist within surviving species as a consequence of introgressive hybridization during eutrophication. Given the prevalence of environmental change, studying speciation reversal and its genomic consequences provides fundamental insights into the evolution of biodiversity, especially its dynamics under environmental change, and informs biodiversity conservation.