Apart from the current human-induced climate change, the Holocene is notable for its stable climate. In contrast, the preceding age, the Pleistocene, was a time of intensive climatic fluctuations, with temperature changes of up to 15 degrees C occurring within a few decades. These climatic changes have substantially influenced both animal and plant populations. Until recently, the prevailing opinion about the effect of these climatic fluctuations on species in Europe was that populations survived glacial maxima in southern refugia and that populations died out outside these refugia. However, some of the latest studies of modern population genetics, the fossil record and especially ancient DNA reveal a more complex picture. There is now strong evidence for additional local northern refugia for a large number of species, including both plants and animals. Furthermore, population genetic analyses using ancient DNA have shown that genetic diversity and its geographical structure changed more often and in more unpredictable ways during the Pleistocene than had been inferred. Taken together, the Pleistocene is now seen as an extremely dynamic era, with rapid and large climatic fluctuations and correspondingly variable ecology. These changes were accompanied by similarly fast and sometimes dramatic changes in population size and extensive gene flow mediated by population movements. Thus, the Pleistocene is an excellent model case for the effects of rapid climate change, as we experience at the moment, on the ecology of plants and animals.