The Upper Castle historic district has been designated as a National Historic Landmark and listed on the National Register of Historic Places. It contains the Indian Castle Church, built in 1769 for the Mohawk by Sir William Johnson, the British Superintendent of Indian Affairs, on land donated by his consort Molly Brant and her brother Joseph Brant, both leaders among the Mohawk. The site also has archeological resources related to Iroquois history. For a time the town was the home of the notable Mohawk leaders Hendrick Theyanoguin (1692–1755) and the Brants. According to Joseph Brant, Canajoharie means "a kettle stuck on a pole." A modern etymology translates it as "a washed kettle". It referred to actions of water from the Mohawk River in a portion of the Canajoharie Gorge.
The modern village of Canajoharie, New York was settled by European Americans a few miles to the east of the historic Mohawk village.