One of the main challenges for conservation today is monitoring and understanding changes in biodiversity. Genetic diversity provides the foundation for biodiversity and is necessary for long-term survival, adaptation, and resilience not only for individuals, but also for populations, species, and entire ecosystems. Monitoring genetic diversity across different time points is a first step to gain insight into the extent to which populations or species might be at risk, to guide conservation action and to provide evidence for solutions. This guidance document aims to be a resource that guides the reader through the decision and evaluation processes that take place when designing a genetic diversity monitoring programme and identifying the most appropriate set of species or populations to monitor. This guidance document is intended for practitioners (including governmental agencies, NGOs, but also locally responsible conservationists such as land managers) who need to monitor genetic diversity of species in the wild.