Although the native Bagratuni dynasty was founded under favourable circumstances, the feudal system gradually weakened the country by eroding loyalty to the central government. Thus internally enfeebled, Armenia proved an easy victim for the Byzantines, who captured Ani in 1045. The Seljuk dynasty under Alp Arslan in turn took the city in 1064.

In 1071, after the defeat of the Byzantine forces by the Seljuk Turks at the Battle of Manzikert, the Turks captured the rest of Greater Armenia and much of Anatolia. So ended Christian leadership of Armenia for the next millennium with the exception of a period of the late 12th-early 13th centuries, when the Muslim power in Greater Armenia was seriously troubled by the resurgent Kingdom of Georgia. Many local nobles (nakharars) joined their efforts with the Georgians, leading to liberation of several areas in northern Armenia, which was ruled, under the authority of the Georgian crown, by the Zakarids-Mkhargrzeli, a prominent Armeno-Georgian noble family.