The earliest history goes back as far as 1605, when Franciscan Friars, under auspices of Spain, established the first of four missions in the southern part of what is now Suwannee County.
The missionaries and soldiers traveled the age-old Indian trails coming into the county from the east near Ichetucknee Springs. This route came to be known as the old Spanish Trail. These missions were destroyed by England around 1800.
In May 1907, the presbyterian congregation moved into a new church, and sold their old building to the diocese. This was moved onto purchased land on Pine Avenue. The church was named St. Margaret Mary’s. No one remembers when the name was changed to St. Francis Xavier. Mass was celebrated on Saturdays when needed.
By 1961, the old church was so deteriorated that mass was discontinued for several months. The congregation then attended mass in either Madison or Lake City. Until the new church was completed in 1962, mass was held in the Live Oak Elks Lodge. The old building was razed and the property sold, as the new church was now located on U.S. 90, on 18 acres of land.