During the spring of 1779, Methodist pioneer Freeborn Garrettson visited this area to bring the message of his faith to the people. Garrettson's efforts were favorably received, and a number of local Methodist "societies" were organized. Among these was the Cedar Neck Society, and it is to this group that the origin of this church can be traced. While local "class meetings" were often held outside or in private residences, for many years members were forced to travel some distance to worship in a church.
On October 1, 1858, the society purchased a small lot of land at this location on which a church was to be constructed. The building was completed and dedicated the following year. The church became known as "Mariner's Bethel" in recognition of the occupation of many of its members. On June 16, 1894, four acres of adjoining land were purchased for the purposes of building a new church and expanding the cemetery. The new building was completed in 1889.
A community hall was added to the sanctuary in 1926, and then replaced with the construction of a new education building that was completed in 1959. The sanctuary's interior and exterior were completely renovated at that time. The education building was subsequently renovated during the time of the construction of a new addition completed in 1995.