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St. Mary's Church was built as a Baptist Seminary in 1835 with funds provided by Gerritt Smith. Smith was a land developer who assisted many communities with construction of their public and religious buildings. The growing Roman Catholic Community of Florence and surrounding area acquired St. Mary's in 1845, establishing a parish of their own. A cemetery was laid out surrounding the church. Many of the stones in the cemetery tell stories of the individual immigrants to the area, noting their place of birth in Ireland. In June 2003 the church was closed, yet due to its popularity has retained its consecration and is designated as a shrine, available for use in funerals and weddings, along with a hugely attended mass once a year.
In October, 2006, due to deteriorating conditions of the lower support beams in the church, a decision to tear down the church was made by the Syracuse Diocese, who owns the building. This church has been considered the oldest Catholic Church in the Syracuse Diocese. No date has been set for demolition.