Juan Antonio Flores Santana (July 3, 1927 – November 9, 2014) was a Roman Catholic archbishop.
Ordained to the priesthood on July 12, 1952, Flores Santana was named bishop of the Roman Catholic Diocese of La Vega, Dominican Republic, on April 24, 1966, and was ordained bishop of June 12, 1966. On June 13, 1992, he was appointed bishop of the Roman Catholic Diocese of Santiago de los Caballeros and then archbishop of the same diocese on February 14, 1994, from which he retired on July 16, 2003.