Santa Maria a Mare stands on the site of the ancient Roman city of Castrum Novum, which later became the medieval center of San Flaviano. The oldest evidence dates back to the 12th century, but it is likely that it was built before the year 1000 and rebuilt on its foundations in the 12th century.

The church has been significantly remodeled and remodeled over time while retaining its Romanesque character. The last restoration, carried out in the 1960s eliminated the 16th and 18th-century additions.