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St. Marys Protestant Episcopal Church was begun on Classon avenue at the Wallabout, by the Rev. D. V. M. Johnson, while in charge of Trinity church. A Sunday school was established in March, 1836, and formed the nucleus of a church. Here the Rev. Mr. Johnson held services on Sunday afternoons for about six months. In May, 1837, Mr. Joseph Hunter took charge of the school, and served as a lay-reader to a small congregation which assembled with the children. During the year an edifice of a very limited extent was erected, and a church organized, to which the name of St. Marys was given. This was consecrated on the first of February, 1840, and was enlarged in 1841, so as to accommodate about two hundred and fifty persons. The parish grew rapidly during the following years, and the church was twice enlarged. In 1856, the Rev. Mr. Johnson, who was originally instrumental in forming the parish, became rector; and as the accommodations were no longer adequate, ground was purchased in the neighborhood, on Classon avenue, near Myrtle, one hundred and sixty-four feet front and two hundred and eighteen deep.

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The corner-stone of a new edifice of brown freestone was laid in the summer of 1858; and the neat and tasteful Gothic structure, designed by Mr. [Richard T.] Auchmuty, fifty-eight fleet wide and one hundred and fifteen feet long, with its tower and spire, and a capacious basement fitted up for the Sunday school, completed in the year following, and opened for divine services on Trinity Sunday. The outlay for ground and church was $32,000; the sittings are free. On the 24th of May, 1862, St. Marys was consecrated by the bishop of the diocese, the Rev. Dr. William F. Morgan, of St. Thomas's church, New York, preaching the sermon.