Thomas Lynch Jr. was an Episcopalian.
From: Robert G. Ferris (editor), Signers of the Declaration: Historic Places Commemorating the Signing of the Declaration of Independence, published by the United States Department of the Interior, National Park Service: Washington, D.C. (revised edition 1975), page 100:
...1776... Although ill himself, Lynch made the onerous trip to Philadelphia. He stayed there throughout the summer, long enough to vote for and sign, at the age of 27, the Declaration of Independence. His father was uanble to take part in the ceremony. The two were the only father-son team that served concurrently in the Continental Congress.
By the end of the year, the failing health of both men compelled them to start homeward.En route, at Annapolis, Md., a second stroke took the life of the senior Lynch. His son, broken in spirit and physically unable to continue in politics, retired to Peach Tree. Late in 1779 he and his wife, heading to southern France in an attempt to regain his health, boarded a ship bound for the West Indies that foundered. The coulde died childless.
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.