In 1649, a third of the village was destroyed in a fire. After the Second War of Villmerger of 1712, the lands of the Freie Ämter were divided into two parts. One section of the new boundary line, extending west from the church in Oberlunkhofen to the "Hochgericht" in Fahrwangen, passed directly through Boswil, with the northern section under control of the Protestant cantons Zürich, Bern and Glarus, and the southern section under control of the catholic cantons. Because of its unique position under the domain of two separate jurisdictions, Boswil's development was constrained. Even with the formation of the Helvetic Republic in 1798, Boswil remained divided between the canton of Baden and the newly formed canton of Aargau, until the two cantons were merged in 1803 as the canton of Aargau. Since then, Boswil has been a part of the Muri district.