Jonathan Dayton was a Presbyterian and an Episcopalian.
He was identified as a Presbyterian by the Library of Congress. A Worthy Company: Brief Lives of the Framers of the United States Constitution by M. E. Bradford was cited as the source stating he was later an Episcopalian. (Source: Ian Dorion, "Table of the Religious Affiliations of American Founders", 1997).
From: Robert G. Ferris (editor), Signers of the Constitution: Historic Places Commemorating the Signing of the Constitution, published by the United States Department of the Interior, National Park Service: Washington, D.C. (revised edition 1976), pages 156-157:
Dayton, youngest of the signers at 26 years of age, lived a busy and adventurous life. A lawyer, land speculator, and Revolutionary soldier, his ambition was unbounded. He held a variety of political offices, including seats in the U.S. House and Senate. He also supported Aaron Burr's ill-fated and murky scheme of 1806 to carve out some sort of empire in the Southwest...
In 1806 illness prevented Dayton from accompanying Aaron Burr's abortive expedition to the Southwest, where the latter apparently intended to conquer Spanish lands and create an empire. Subsequently indicted for treason, Dayton was not prosecuted, but could not salvage his national political career. He remained popular in New Jersey, however, continuing to hold local offices and sitting in the assembly (1815-15).
...He was laid to rest at St. John's Episcopal Church in his hometown. Because he owned 250,000 acres of Ohio land between the Big and Little Miami Rivers in the vicinity of the site of Dayton, the city was named after him--his major monument.
Note that numerous sources and authoritative references have been consulted in order to ascertain the religious affiliation of the American Founding Fathers. Note that the excerpts and references mentioned on this page are not the only references used in order to identify this person's religious affiliation.