SignificanceNative rodents represent 41% of Australian mammal extinctions since European colonization. To determine the scale and timing of their decline, we used museum specimens to generate genome-scale data from eight extinct Australian rodents and their 42 living relatives. Relatively high genetic diversity in extinct species immediately prior to extinction in the 19th or 20th century indicates that their populations were previously large and that declines began after European colonization of Australia. This demonstrates that genetic diversity does not necessarily provide insurance against catastrophic extinction events. Our results show that extinction risk was elevated for larger-bodied rodents and varied among biomes. In addition, we taxonomically resurrect an extinct species, Gould’s mouse, which survives on an island in Shark Bay, Western Australia.