Conservation genetics is often focusing on species of immediate conservation concern, and therefore has largely implemented single-species approaches. However, the increasing anthropogenic impact on natural systems may put multiple species sharing the same environments at risk. This is triggering the development of (comparative) multi-species approaches in conservation genetics – a development facilitated by the increasing capacity of molecular methods. Such approaches offer the opportunity to identify the degree of concordance (or discordance) in population structure across species, as well as the possibility to compare species-specific adaptive responses. Ultimately, a shift in focus from single species to communities may improve biodiversity conservation in heterogeneous landscapes. In my presentation, I will give an overview of these developments, and illustrate with examples of riverine fishes how they may support conservation and management.