We reconstructed changes in the Cryptomeria japonica forest during the Holocene through pollen analysis of peat sediments collected from Akita Prefecture. Ancient documents recording past landscape use and human activity near the sampling sites were compared to reconstruct vegetation change. C. japonica was present to some degree at the beginning of the Holocene. The expansion of C. japonica occurred after 3000 cal BP at most sites. We consider that some small C. japonica groups, scattered near the sites, expanded with increasingly humid conditions. A recent decrease in C. japonica began ca. 500 cal BP of the Muromachi Period at most sites. It was associated with increases in diploxylon pines and herbaceous taxa. Moreover, results showed that Fagopyrum was cultivated at some sites. From comparison with historical documents and vegetation change, human influences, such as agriculture and timber utilization, began to increase in the end of the Muromachi Period around the Akita region.