Here we demonstrate the successful extraction and amplification of target species DNA from artefacts made of whale baleen collected from excavations of past palaeo-Eskimo and Inuit cultures in Greenland. DNA was successfully extracted and amplified from a single baleen bristle of 1.5 cm length dated based on archaeological context to the period of the Saqqaq culture, more than 4000 years ago and following decades of storage at room temperature at the National Museum. The results reveal ancient baleen in archaeological material as a potential source of DNA that can be used for population genetic studies. We conclude that genetic investigation of historical baleen collections can contribute to our knowledge of the prehistoric population genetics of baleen whales, for example by quantifying the impact of modern whaling on the genetic diversity of bowhead whales.