Kenozero was always a remote area. In the 19th century, the area was divided between Pudozhsky Uyezd (west) and Kargopolsky Uyezd (east) of the Olonets Governorate. In Soviet Union, after a number of administrative changes, the area ended up in the Arkhangelsk Oblast. In 1950s—1980s, as everywhere in Russian North, the area suffered severely from depopulation, in particular, all villages between Lake Lyokshmozero and Lake Kenozero were deserted.

In 1991, the decision was taken to create a National Park in the area. All historical monuments were transferred to the park administration, and some of them have been restored. December 28, 1991 the park was officially created. The staff of the park at the time of creation was 7 persons. In 1992 it was increased to 35 persons, and in 1993 to 153. In 2004, the park became a UNESCO Biosphere Reserve.