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Integrative and proactive conservation approaches are critical to the long-term persistence of biodiversity. Molecular data can provide important information on evolutionary processes necessary for conserving multiple levels of biodiversity (genes, populations, species, and ecosystems). However, molecular data are rarely used to guide spatial conservation decision-making. Here, we bridge the fields of molecular ecology (ME) and systematic conservation planning (SCP) (the 'why ') to build a foundation for the inclusion of molecular data into spatial conservation planning tools (the 'how'), and provide a practical guide for implementing this integrative approach for both conservation planners and molecular ecologists. The proposed framework enhances interdisciplinary capacity, which is crucial to achieving the ambitious global conservation goals envisioned for the next decade. Molecular ecology (ME) and systematic conservation planning (SCP) have seen rapid technological advancements in recent decades, but the use of molecular data to conserve different aspects of biodiversity remains operationally illusive. Here, the core principles of ME and SCP are combined in a novel way, showcasing how themes and corresponding data types from each field can complement each other. A framework, including five practical steps, is provided to guide both molecular ecologists and conservation planners to build systematic conservation plans that effectively integrate evolutionary features. [ABSTRACT FROM AUTHOR]