Houghtaling was born in New Baltimore, New York in 1763. He was a son of Capt. Thomas Houghtaling (1731–1824) and Elizabeth (née Whitbeck) Houghtaling. Among his siblings were brothers Hendrick Houghtaling (who married Elizabeth Staats), Andries "Andrew" Houghtaling (who married Polly N. Van Benthuysen) and sister, Hester Houghtaling, was the wife of Peter A. Van Bergen (the brother of his wife). His father fought in the second Battle of Saratoga under Lt.-Col. DuBois and Col. Anthony Van Bergen, who led the 11th Regiment of the Albany County militia in the Revolutionary War.