Mariners’ Temple Baptist Church stands on the oldest site for Baptist worship on Manhattan Island. In 1795, Henry Rutgers (1745–1830), a descendant of Dutch immigrants, a former colonel in the Revolutionary War, and a philanthropist with considerable land holdings in Manhattan, donated land at Oliver and Henry Streets to the American Baptist.  Baptists have worshiped continuously at this site ever since.

The first Church at Oliver and Henry Streets was called the Oliver Street Meeting House.  It was located only a few blocks from the first White House on Cherry Lane, which was occupied by George Washington and his wife. Diagonally across the street from the Meeting House was the first free school for African Americans, now known as Public School 1.  

The early Church began as a mission for seamen who docked at the nearby East River. The church became famous for the massive steel bell in the tower, which called for the seamen and community residents to worship. However, with the development of steam power, bigger ships needed the deeper waters of the Hudson River and maritime activity shifted westward. 

In 1822 the Fayette (Street) Baptist Church moved to the Oliver and Henry Street site and renamed itself the Oliver Street Church. In 1832, the Sixth Triennial Meeting of the Baptist Missionary Society was held at the Oliver Street Meeting House.  The American Baptist Home Mission Society was organized at this meeting.
According to an account written by Rev. Ira R. Steward, the first pastor of Mariners’ Temple, the New York Domestic Missionary Society decided to launch a ministry for seamen in the spring of 1841. A hall at the Corner of Cherry and Catherine Churches was secured in which to hold services. They hired Mr. John Wivil, an Englishman who had been a sailor, to serve as Chaplain. He was dismissed after eight months. After several months with spiritual leadership, Elder Jones of Newburg was hired, and was eventually succeeded by Elder Betham of Orange.

Around this time, an appeal was made in the Oliver Street Meeting House to form a Bethel society, which would be comprised of females in New York and the neighboring vicinity. From this appeal, the Baptist Female Bethel Union was formed. Their goal was to bolster the moral and spiritual welfare of the seamen in the city.

Members and supporters of the Union soon realized that in order for the ministry to be effective, a church was needed. In May 1842, a church of twenty members was organized on the condition that one George Benedict would be called as Pastor. However, the effort to obtain Benedict failed, and the enterprise languished until the spring of 1843, when the Bethel Union once again obtained the hall at Catherine and Cherry Streets and opened it for worship on the first Sunday in May of 1843. Brother John Cook, a licentiate from Macdougal Street Baptist Church was secured to serve as Chaplain. That summer five people received Christ as their Savior.