Paleogenomics, also known as genome-wide ancient DNA analysis, is transforming our understanding of the human past, but has been much less intensively used to understand the history of other species. However, paleogenomic studies of non-human animals and plants have the potential to address an equally rich range of evolutionary, paleoecological, paleoenvironmental, and archaeological research questions. Three recent case studies of cave bears, horses, and maize provide examples of the ways that paleogenomics can be used to examine potential causes of extinctions and dynamic processes of domestication. Much more research in these areas is needed, and we conclude by highlighting key future directions. To date, genome-wide analyses of ancient organisms have primarily focused on humans, despite the fact that there are millions of living and extinct plant and animal species that also can be studied with these techniques. Natural history museums, archives, and archaeological collections harbor abundant sources of ancient DNA for studying past plant and animal genetic diversity around the world. Ancient DNA provides access to genomic data covering hundreds of thousands of years, allowing for the investigation of evolutionary, ecological, social, and environmental questions in deep time, especially regarding the ways that humans have interacted with other species and modified past ecosystems and environments. Case studies of cave bears, horses, and maize highlight the power of paleogenomic data to shed light on extinctions, admixture between domestic and wild animals, and the gradual selection for domestication genes during plant and animal domestication. It is time to apply the power of genome-wide ancient DNA analysis to non-humans as ambitiously as it has been applied to our own species, making sure to treat ancient specimens in an ethical way that preserves them for future generations.