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Bronze and Iron Age artifacts have been discovered in the area of this ancient site, some dating to the Anaeolithic (Copper) Age.
The origin of its name is believed to be a combination of Georgian (“kob”) and Armenian ("aiyr"), word roots for cavern—indeed, the surrounding hills are full of caves.
Kobaiyr was home to the 12th century chronicler David Kobaiyretsi and mentioned by the chronicler Vartan Areveltsi and others as an important center of writing and culture in the mid 13th century. Its history is closely connected to some of the most famous medieval Armenian feudal houses - the Kiurikians, the Bagratunis and the Zakarians, the latter of which brought Chalcedonian congregations to Kobaiyr in the mid 13th century and introduced a new style of architecture, including a rich fresco style inside the churches.
The complex’s main entrance (6) has a vaulted 'tunnel' with cylindrical towers. The main church, the late 12th century Katoghike (Cathedral, 1) is a partially ruined single nave church that is undergoing restoration. The main entry was decorated with an intricately carved door frame, the façade crowned with a frieze carved with ornamental details, rosettes and geometric patterns. The church's most famous features, though, are the magnificent frescoes that are still preserved.
The frescos on the apse are in three rows: the Virgin Mary and archangels at the top, the Eucharist in mid-row and figures of saints and prophets underneath. The chapel had frescos as well, in the same three-row composition of Christ enthroned, the Eucharist, and saints. Portraits of sponsors are on the western wall and the lower row of the northern wall.
Next to the Katoghikeh, the smaller half-ruined Mariamashen Church (2) stands on the edge of the cliff and is the oldest structure of the complex. According to an inscription at the entrance it was built for Mariam, daughter of King Kiurikeh II in 1171.
The belfry/sepulcher (3) is north of the Katoghikeh, in the middle of the complex, a square hall with an eastern Apse taking up the entire wall. According to a Georgian inscription on the southern wall, Amirspasalar Shah’n’shah's son Mkhargrdzeli and his wife Vaneni ordered the construction of the belfry. It is dated 1279.
West of the belfry are the partial ruins of the 13th century refectory (4), a rectangular hall with just its walls and some of the vaulted roof surviving.
The remains of a 12th century single-nave church (5) with vaulted ceiling and a tunnel lie to the north of the refectory. Near the church there are the remains of a small chapel.