The preservation of genetic diversity is an important aspect of conservation biology. Low genetic diversity within a population can lead to inbreeding depression and a reduction in adaptive potential, which may increase extinction risk. Here we report changes in genetic diversity over 12 years in a declining population of the Corncrake Crex crex, a grassland bird species of high conservation concern throughout Europe. Despite a twofold demographic decline during the same period, we found no evidence for a reduction of genetic diversity. The gradual genetic differentiation observed among populations of Corncrake across Europe suggests that genetic diversity is maintained in western populations by constant gene flow from the larger and more productive populations in eastern Europe and Asia. The maintenance of genetic diversity in this species is an opportunity that may help the implementation of effective conservation actions across the Corncrake’s European range.