Small sardine-like freshwater fishes hold the potential to feed millions of people in the Global South. Yet, the biological mechanisms underlying the adaptation and resilience of these fishes to climate change and fishing pressure are poorly understood. Genetic approaches can provide valuable insights into stock structure, demography and evolutionary potential of fish populations, which can be used to prevent overfishing. Despite the importance of this information, it is often still lacking in fisheries management, especially in developing countries. We aim to obtain this knowledge for the freshwater sardines Stolothrissa tanganicae and Limnothrissa miodon, two important fisheries targets of Lake Tanganyika. Ultimately, we will use our research results to evaluate stakeholder concerns, enabling the proposition of an adapted management plan, serving as a model system for sustainable fisheries in tropical freshwater lakes.