When the Arabs conquered Egypt in 641, they found a deeply divided Christian church – in fact what they found amounted to two quite separate churches. They are usually called, in neutral terms, ‘Chalcedonian’ and ‘anti-’ or ‘non-Chalcedonian’, with reference to the Council of Chalcedon where their split had been consummated two centuries earlier. The two churches disagreed deeply on Christological questions, and during the two centuries that followed the Council, there were several, often heavy-handed, attempts to bring the non-Chalcedonian churches back into the imperial sphere. These events are unfortunately known mainly from polemical sources from both sides, and although this last fact does allow us to get a more balanced view, it also creates the impression that the Chalcedonian conflict dominated life in the Empire after the fifth century, an impression that certainly needs qualification.

In Egypt, the non-Chalcedonian or Monophysite church modelled itself on the highly centralised structure of the existing patriarchate of Alexandria, which, contrary to the other four patriarchates, did not have an intermediate level of metropoles between the patriarch and the local bishops. Both churches had their leaders in Alexandria, heading two welldeveloped parallel networks of episcopal sees and affiliated monasteries which covered most of the valley. In 641, the Chalcedonian church had, for over a century, been actively backed by the imperial power structure, often forcing the non-Chalcedonian hierarchy to leave the city centres and retreat to monasteries from where they managed their communities. The political break with Constantinople brought about by the Arab conquest eventually weakened the position of the Chalcedonian Church.