Abstract Patterns in phenotypic and genotypic diversity within many species are becoming increasingly apparent, although there remain many species for which such patterns have yet to be described adequately. Fishes from recently glaciated ecosystems are likely to be particularly rich in intraspecific diversity, yet current conservation management strategies are, in many parts of the world, particularly in Europe, conventionally and overwhelmingly focused on species, regardless of competing species concepts, and appropriate policies for managing diversity at a sub‐specific level still have to be developed. Occasional attempts to protect certain vulnerable ecotypes and proposed alternative units of conservation (e.g. ‘Pragmatic Species’ or ‘Evolutionarily Significant Units’) reinforce the conventional primacy of contemporary expressed patterns of variation. Intraspecific phenotypic and genotypic patterns are ultimately the result of complex processes of divergence; conservation approaches that focus on the products of evolution largely ignore the processes that generate and maintain those patterns. Policies that acknowledge the continuation of evolution, the derivation of novel diversity over often very short time spans and the role of environment in initiating and perpetuating these processes are poorly integrated into management strategy. To address possible deficits, where intraspecific diversity is not addressed in management practice, we believe it to be important first to characterize hidden genetic and phenotypic diversity, which may intimate eco‐evolutionary processes, initially among species of high conservation status. A second step should be to use an approach to intraspecific diversity that illuminates the ultimate processes and mechanisms that bring about that diversity, which also concedes the central role of the environment and affords adequate protection to the ecosystems that drive these processes, such as the United Nations Convention on Biological Diversity (CBD) Ecosystems approach.
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