Unknown is the date of construction of the original church, built to guard the remains of the saint, which were moved to Bovino perhaps to secure them after the destruction of Aeca in 663. Nothing is known about the origin of the church of San Marco, except that it was consecrated in 1197, as attested by an epigraph dated 1703, and annexed to the presbytery of the then cathedral.
The current appearance of the church is due to the restorations that took place during the 1930s of the 20th century, which eliminated all the Baroque additions, preserving only the eighteenth-century altar on which insists the altarpiece with the "Vision of St Mark" and a bust of Neapolitan school reliquary of the eighteenth century. containing the bones of the saint.
The interior has a single nave, closed by a large presbytery, surmounted by a dome. Along the walls of the nave are four sepulchral monuments of bishops of the city. Of fine workmanship is then the marble baptismal font of the seventeenth century, gift of the Guevara.
The Cappellone is also accessible from the outside through a portal with a bas-relief lunette depicting St. Mark of Aecae, with mitre and pastoral, between two deacons, who hold the liturgical ornament.