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As the Anthropocene progresses, increasing numbers of species and populations face the threat of extinction due to widespread habitat loss, climate change, environmental degradation, and other stressors. In order to mitigate this threat, it is critical to understand the genetic diversity that makes a population resilient in the face of change. Recent advances in sequencing technology have dramatically improved this understanding, enabling the precise application of management approaches. Habitat regions with high genomic diversity can be protected and connected with wildlife corridors, while regions with low genomic diversity can be targeted for improvement through translocation. Meanwhile, genomic, transcriptomic, and epigenomic data reveal signatures of local adaptation and responses to stressors. These signatures further inform conservation strategies, for example the use of gene editing to help species cope with new conditions. This Collection will highlight research seeking to understand patterns of genetic diversity at all levels in order to further conservation goals.