Under Justinian the pagan schools were again and from that time forward closed. Isidorus the platonist and Salustius the Cynic were among the learned men of greatest note who then withdrew from Alexandria. Isidorus had been chosen by Marinus as his successor in the platonic chair at Athens, to fill the high post of the platonic successor; but he had left the Athenian school to Zenodotus, a pupil of Proclus, and had removed to Alexandria. Salustius the Cynic was a Syrian, who had removed with Isidorus from Athens to Alexandria. He was virtuous in his morals though jocular in his manners, and as ready in his witty attacks upon the speculative opinions of his brother philosophers as upon the vices of the Alexandrians. These learned men, with Damascius and others from Athens, were kindly received by the Persians, who soon afterwards, when they made a treaty of peace with Justinian, generously bargained that these men, the last teachers of paganism, should be allowed to return home, and pass the rest of their days in quiet.
After the flight of the pagan philosophers, but little learning was left in Alexandria. One of the most remarkable men in this age of ignorance was Cosmas, an Alexandrian merchant, who wished that the world should not only be enriched but enlightened by his travels. After making many voyages through Ethiopia to India for the sake of gain, he gave up trade and became a monk and an author. When he writes as a traveller about the Christian churches of India and Ceylon, and the inscriptions which he copied at Adule in Abyssinia, everything that he tells us is valuable; but when he reasons as a monk, the case is sadly changed. He is of the dogmatical school which forbids all inquiry as heretical. He fights the battle which has been so often fought before and since, and is even still fought so resolutely, the battle of religious ignorance against scientific knowledge. He sets the words of the Bible against the results of science; he denies that the world is a sphere, and quotes the Old Testament against the pagan astronomers, to show that it is a plane, covered by the firmament as by a roof, above which he places the kingdom of heaven. His work is named Christian Topography, and he is himself usually called Cosmas Indicopleustes, from the country which he visited.
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.
The Emperor Mauricius was murdered by Phocas, who, in 602, succeeded him on the throne of Constantinople. No sooner did the news of his death reach Persia than Chosroes, the son of Hormuz, who had married Maria, the daughter of Mauricius, declared the treaty with the Romans at an end, and moved his forces against the new emperor, the murderer of his father-in-law. During the whole of his reign Constantinople was kept in a state of alarm and almost of siege by the Persians; and the crimes and misfortunes of Phocas alike prepared his subjects for a revolt. In the seventh year Alexandria rebelled in favour of the young Heraclius, son of the late prefect of Cyrene; and the patriarch of Egypt was slain in the struggle. Soon afterwards Heraclius entered the port of Constantinople with his fleet, and Phocas was put to death after an unfortunate reign of eight years, in which he had lost every province of the empire.
During the first three years of the reign of Heraclius, Theodoras was Bishop of Alexandria; but upon his death the wishes of the Alexandrians so strongly pointed to John, the son of the prefect of Cyprus, that the emperor, yielding to their request, appointed him to the bishopric. Alexandria was not a place in which a good man could enjoy the pleasures of power without feeling the weight of its duties. It was then suffering under all those evils which usually befall the capital of a sinking state. It had lost much of its trade, and its poorer citizens no longer received a free supply of grain. The unsettled state of the country was starving the larger cities, and the population of Alexandria was suffering from want of employment. The civil magistrates had removed their palace to a distance. But the new bishop seemed formed for these unfortunate times, and, though appointed by the emperor, he was in every respect worthy of the free choice of the citizens. He was foremost in every work of benevolence and charity. The five years of his government were spent in lightening the sufferings of the people, and he gained the truly Christian name of John the Almsgiver. Beside his private acts of kindness he established throughout the city hospitals for the sick and almshouses for the poor and for strangers, and as many as seven lying-in hospitals for poor women. John was not less active in outrooting all that he thought heresy.