John F. Webber, an Anglo, settled in this area with his African American wife and children after receiving a land grant in 1827. Webber sought to find a place where he and his family could escape the discrimination of the antebellum South. The resulting community eventually received a post office and was known originally as Webber's Prairie. The town officially adopted the name Webberville in 1853. Cotton brought prosperity to this small community, which boasted almost 400 residents by the turn of the century and included cotton gins, grist mills, four general stores, two churches, a cemetery and several schools. As time passed, however, the community began to shrink, and the post office closed in 1903.

The Webberville Ebenezer Baptist Church was founded in 1868, when resident Matthew Duty donated land for the sanctuary construction. Led by the Rev. Wesley Barrow, the church was formed as a mission of the St. John Regular Missionary Baptist Association. Although many of Webberville's former citizens have moved, the church boasts an active congregation; out-of-town members continue to gather to celebrate holidays and special events. When visiting the church, look to the north, across an open pasture, for an iron fence surrounding a few stone markers; this is Duty's cemetery, where he and several members of his family were buried in the 1800s.