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Also called the "Gothic Church", the Second M. E. Church of Williamsburgh was organized on 4 September 1845 with ten members. The cornerstone for the church was laid on 4 December 1845 and the church was dedicated on 26 November 1846. The original trustees included Daniel Maujer, Lemuel Richardson, John F. Luther, Robert G. Thursby, Isaac Henderson and Charles Maujer.

The Zion A. M. E. Church of Williamsburgh was organized in 1832 by Thomas Watson, in his house on Third (Berry) Street between North 4th and North 5th Streets. The church later rented rooms on North 4th Street between Third and Fourth Street (Berry and Bedford). The congregation numbered 12 members at this time, and retained Rev. John Churchill as its first regular preacher. Churchill also taught at the African Free School (later Colored School No. 3).

Organized on 18 June 1842 and Incorporated in 1844. William Harden, a blind Black preacher was the first and only leader of the church. The first place of worship was in a rope walk, and after that burned the congregation met in private houses. After Harden's death in 1847, the congregation split up, with most of the worshippers moving over to the African M. E. Church on High Street.

Organized in 1839 by a group of parishioners from Washington Street M. E. Church who were dissatisfied over the appointment of a preacher. Originally called the Centenary M. E. Church in honor of the centenary of Methodism in 1839, the congregation changed its name to the Johnson Street M. E. Church in 1868. The first church for the congregation was constructed in 1840 at a cost of $8,000.

The first effort to organize the Dekalb Avenue M. E. Church began in the fall of 1836 with private services at the home of John Robb on Flushing Avenue near Classon Avenue. The first sermon was preached on 18 June 1837 in a school house on Classon Avenue, and the Sabbath school was established on the same date.

This congregation was a spin-off from Sands Street M. E. Church. On 18 January 1818 the church was incorporated as a satellite of the Sands Street M. E. Church, after the number of Black congregants at that church exceeded the capacity of the "colored gallery" there. In 1819, the trustees of Sands Street imposed a fee of $10 per quarter on the Black worshippers, compelling the majority of them to secede to form their own church. The first trustees for the congregation were Peter Cruger, Israel Jemison, Caesar Sprong, Benjamin Cruger and John E. Jackson.