The Town of Fayette is on the western border of the county and is southeast of Geneva, New York.
Seneca was part of the Central New York Military Tract and was first settled around 1790.
The town was established from part of the Town of Romulus in 1800 as the "Town of Washington," but adopted the current name in 1803.
In Fayette on April 6, 1830 Joseph Smith, Jr., who was from nearby Palmyra, New York, organized the Church of Christ, later to be known as the Church of Jesus Christ of Latter Day Saints, in a log home owned by Peter Whitmer, Sr.. Whitmer was one of five others besides Smith who where the initial six members.
In 1980 this reconstructed log home, built on the site of the original Whitmer home, was dedicated as part of the sesquicentennial celebrations of The Church of Jesus Christ of Latter-day Saints (LDS Church). The dedication was done by then LDS Church President Spencer W. Kimball and was broadcast by satellite, as part of the semi-annual church General Conference, to many LDS stake centers around the world. The Whitmer log home continues to be operated as a religious historical site by the LDS Church.