Volcanic islands provide notable examples of the parallel between a changing geographic area and its changing biota. This is particularly true for young islands where volcanic activity is known to dictate the rate of population extinction and recolonization and to influence evolutionary diversification. However, examples of demographic changes associated with historical volcanism are hard to describe because of difficulties in extracting information about population history. Here, we show that genes of a giant tortoise population have recorded a signature associated with a sizable prehistoric eruption of Volcano Alcedo on the Galapagos Islands.