The Église Saint-Bénigne in Pontarlier is a church dating from the 15th, 16th and 17th centuries. This church combines Romanesque, Gothic and Franc-Comtoise style elements. The striking clocher porch is topped with an imperial domed roof, also known as a clocher comtois, a traditional feature of Franche-Comté. The roof is covered with glazed tiles. The Église Saint-Bénigne is located in the Haut-Doubs and is dedicated to Saint Bénigne. Since May 19, 1970, the building has been registered as a historical monument.
Historically, the church was almost completely rebuilt between 1651 and 1666 on the same site as an original 11th century Romanesque church, of which almost nothing remains (except a 15th century portal). This happened after the passage of the troops of Duke Bernard de Saxe-Weimar during the Thirty Years' War. In 1666 the church was rededicated in honor of Saint Bénigne. The church has suffered serious damage over time from two fires, one in 1680 and one during the Pontarlier fire of 1736. The clocher porch was rebuilt in 1681, and the imperial dome was added in 1753 by architect Nicolas Nicole. In 1970 the church underwent a major restoration, and in 1974 new stained glass windows were created by artist Alfred Manessier and the Lorin de Chartres workshops.
The organ, which dates from 1758 and is in Louis XV style, was restored in 1844 and again in 1982.