It was the site of two notable medieval battles between Byzantines and Bulgarians, the Battle of Marcellae of 756 and the Battle of Marcellae of 792.
Markeli acquired its strategic importance in the late 7th century, when the establishment of the First Bulgarian Empire and its expansion turned it into a vital frontier stronghold just south of the Balkan Mountains.
The fortifications were constructed out of crushed stones with integrated rows of bricks and are thought to date to the reign of either Anastasius I (491–518) or Justinian I (527–565), i.e. The ramparts were up to 10 metres (33 ft) high and had over 3-metre (9.8 ft) ditches before them.
Markeli is situated near the Mochuritsa River (a major tributary of the Tundzha), on the western tip of the Hisar highland, which is part of the southeastern Balkan Mountains.The defensive wall is thought to have been 6 to 8 m (20 to 26 ft) tall.The Elensko area where the church is located (and which was the basis for its name) was known to have been inhabited in antiquity by a Thracian tribe, who around the 6th–5th century BC joined the Bessi state.The Ottomans reportedly bombarded the church with cannons and set it ablaze because they regarded the monks as rebellious.The earliest archaeological research on the Elenska Basilica dates to the 1890s, when local teachers explored the ruins.