During the latter years of the government of Apollinarius, such was his unpopularity as a spiritual bishop that both the rival parties, the Gaianites and the Theodosians, had been building places of worship for themselves, and the more zealous Jacobites had quietly left the churches to Apollinarius and the Royalists.  But on the death of an archdeacon they again came to blows with the bishop; and a monk had his beard torn off his chin by the Gaianites in the streets of Alexandria.  The emperor was obliged to interfere, and he sent the Abbot Photinus to Egypt to put down this rebellion, and heal the quarrel in the Church.  Apollinarius died soon afterwards, and Justinian then appointed John to the joint office of prefect of the city and patriarch of the Church.  The new archbishop was accused of being a Manichean; but this seems to mean nothing but that he was too much of the Egyptian party, and that, though he was the imperial patriarch, and not acknowledged by the Koptic church, yet his opinions were disliked by the Greeks.  On his death, which happened in about three years, they chose Peter, who held the Jacobite or Egyptian opinions, and whose name is not mentioned in the Greek lists of the patriarchs.  Peter’s death occurred in the same year as that of the emperor.

Under Justinian we again find some small traces of a national coinage in Egypt.  Ever since the reign of Diocletian, the old Egyptian coinage had been stopped, and the Alexandrians had used money of the same weight, and with the same Latin inscriptions, as the rest of the empire.  But under Justinian, though the inscriptions on the coins are still Latin, they have the name of the city in Greek letters.  Like the coins of Constantinople, they have a cross, the emblem of Christianity; but while the other coins of the empire have the Greek numeral letters, E, I, K, A, or M, to denote the value, meaning 5, 10, 20, 30, or 40, the coins of Alexandria have the letters 1 B for 12, showing that they were on a different system of weights from those of Constantinople.  On these the head of the emperor is in profile.  But later in his reign the style was changed, the coins were made larger, and the head of the emperor had a front face.  On these larger coins the numeral letters are [A r] for 33.  We thus learn that the Alexandrians at this time paid and received money rather by weight than by tale, and avoided all depreciation of the currency.  As the early coins marked 12 had become lighter by wear, those which were meant to be of about three times their value were marked 33.

During the period from 566 to 602 Justin II. reigned twelve years, Tiberius reigned four years, and Mauricius, his son-in-law, twenty; and under these sovereigns the empire gained a little rest from its enemies by a rebellion among the Persians, which at last overthrew their king Chosroes.  He fled to Mauricius for help, and was by him restored to his throne, after which the two kingdoms remained at peace to the end of his reign.