After several years of ministry, seven men and six women organized themselves into an independent church, the Baptist Seamen’s Bethel. However before they became incorporated, the members unanimously voted to change the church’s name to “First Baptist Mariners’ Church, New York City.” Of the church’s original thirteen members, ten were from Macdougal Street Baptist Church, including one deacon, one trustee, the first directors of the Bethel Union, and the chaplain; two from Oliver Street, and one from Cannon Street. None were from the twenty members that had organized in 1842.
On December 4, 1843, a council from most of the Baptist churches in New York and Brooklyn met in the Oliver Street Baptist Meeting-house. Dr. S.H, Cone, served as the moderator for the gathering. At that meeting, it was unanimously resolved to extend to First Baptist Mariners’ fellowship as a sister church.
Once the First Baptist Mariners’ was organized, Brother Cook agreed to continue as the church’s chaplain until they could find someone more experienced to serve as the pastor. As the congregation prayed that God would direct them to the right person, some ministers recommended Elder Ira R. Steward of Mystic, Connecticut, who was once a seaman, for the pastorate. Meanwhile, the Home Mission Society introduced Elder David Morris to serve the congregation on an interim basis.
During Elder Morris’s brief tenure, Elder Steward came to worship with the First Baptist Mariners’ congregation and, as a result, a unanimous call was extended for Steward to become their pastor. Despite being “harmoniously connected for 11 years, during which he had baptized four-fifths of the congregation,” the church in Groton, Connecticut, where Steward was serving as pastor “believed it to be their duty to give him up to engage in this important enterprise, for which they considered him to be peculiarly adapted on account of having associated so long with that class of men prior to entering the ministry.”
By 1848, the Cherry and Catherine Street hall, which measured twenty-five by fifty feet, had become too small for its congregation. It was crowded, close, and poorly ventilated, which negatively impacted Steward’s health. A joint committee of seventy brethren from Baptist churches in New York came together and resolved to build First Baptist Mariners’ a church. However, after a year with little results, the committee gave up the enterprise to an association known as “The Mariners’ Church Society.” The society existed to two years before it disbanded, having also failed to accomplish its goal. The work was turned over to the trustees of the First Baptist Mariners’ Church, along with a lot that had been secured on Cherry Street between Pike and Rutgers and funds that had been collected. In November 1848, the congregation entered into the lecture-room of their new chapel, which cost $11,000 to complete, Steward described the chapel as being “sixty feet wide by seventy-six long, surmounted by a neat tower and flagstaff, about 105 feet high, and when finished will seat about 100 persons.”
The congregation again outgrew its space and sold the Cherry Street chapel for $9,000. In 1863 (1866?), First Mariner’s purchased the Church building on the oldest Baptist ground at Oliver and Henry Streets for $32,000. The house of worship became internationally known as either the Baptist Mariners’ Temple or The Mariners’ Temple. In 1867, a special act of the New York State Legislature transferred the Church property to the American Baptist Home Mission to hold in trust for the First Baptist Mariners' Church. The pews were free forever. This legal action was instituted to make Mariners' a permanent place of worship for seamen.