Complex host–vector–virus interfaces can impose serious health challenges. Western honeybees have experienced high colony losses globally, mainly driven by the host-shifted, virus-vectoring ectoparasitic mites Varroa destructor and Tropilaelaps mercedesae. Host populations can survive mite infestations through natural selection, offering a long-term strategy for colony health. However, host–vector–virus coevolution requires local adaptations of this triad, which is poorly understood. We propose harnessing natural selection through a global approach focused on standardized monitoring of colony survival, mite infestation levels, and control of reproductives. Studying native and adapted mite hosts, host shifts, and comparing susceptible to surviving hosts will enhance understanding of this host–vector–virus system. This strategy promotes colony health in both managed and wild host populations and provides insights into other host–vector–virus interfaces.