A few of the bishops who helped spread Christianity on the island were Lazarus, the Bishop of Kition, Herakleidios the Bishop of Tamasos, Avxivios the Bishop of Soloi, and Theodotos the Bishop of Kyrenia.
Towards the end of the 4th century, Christianity had spread throughout the island. During this time St. Epiphanius was Archbishop. His seat was in Salamis, which was renamed Constantia.
This independent position by ancient custom was recognized, against the claims of the Patriarch of Antioch, at the Council of Ephesus (431 CE), and by an edict of the Byzantine Emperor Zeno. When the Archbishop of Antioch tried to abolish the Church of Cyprus' autocephaly, the Cypriot clergy denounced this before the Third Ecumenical Synod, which convened in 434 AD in Ephesos. The Synod ratified the autocephaly of the Church of Cyprus by its 8th canon.
In 478 AD, Archbishop Anthemios of Cyprus, following a vision, found the grave of St. Barnabas and his relics. On the saint's chest rested a copy of the Gospel of Matthew. The church was thus able to send a cogent argument on its own behalf to the Emperor: the discovery of the relics of its reputed founder, Barnabas. Zeno confirmed the status of the Church of Cyprus and granted its Archbishop the "three privileges": namely to sign his name in cinnabar, an ink made vermilion by the addition of the mineral cinnabar; to wear purple instead of black robes under his vestments; and to hold an imperial sceptre (i.e. a gilt staff of silver, topped by a gold globus cruciger) instead of the regular episcopal crosier.
Cyprus suffered greatly from Arab invasions in the following centuries, and during the reign of Justinian II the cities of Salamis (Constantia), Kourion and Paphos were sacked. At the advice of the Emperor, the Archbishop fled to the Hellespont along with the survivors, and established the city of Nova Justiniana (Greek: Νέα Ιουστινιανή, Néa Iustinianē), named after the Emperor, near the city of Cyzicus. In 692 the Quinisext Council (also called "in Trullo") reconfirmed the status and privileges of the exiled Archbishop and in 698, when the Arabs were driven out of Cyprus, the Archbishop returned but retained the title of "Archbishop of Nova Justiniana and All Cyprus": a custom that, along with the "three privileges", continues to this day.
The Franks were succeeded by the Venetians in 1489 without any significant change to the status of the Orthodox Church.
The conquest of Cyprus by the Ottoman Empire in 1571 led to the recognition of the Orthodox church as the only legal Christian church. The church was considered by the Ottomans to be the political leadership of the Christian population (Rum millet) and was responsible for collecting taxes. Because of the different policies of the Ottoman empire towards Muslim and non Muslim citizens, especially regarding taxation, some Christians converted to Islam. These are known in Cyprus with the name "Linopampakoi".
Attempts were made subsequently by the patriarchs of Antioch to claim authority over the Cypriot Church, the last as recently as 1600, but in vain.
Nevertheless, during the Ottoman period (1571-1878) Cyprus went through hard times. People lived in insecurity and their life and property was constantly at the disposal of the Ottomans. The role of the Church in the preservation of faith, national identity and traditions of orthodox Greek Cypriots was particularly important. The churches were not mere places of worship but were transformed to schools and places of ethnic inspiration.
The revolution in Greece in 1821, together with information of a revolutionary movement in Cyprus, resulted in the execution of Archbishop Kyprianos on 9 July 1821 and Bishops Chrysanthos of Paphos, Meletios of Kitium, Lavrentios of Kyrenia, of the Abbot Josef of the Kykkos Monastery and other notables, clergymen and common people.
In 1872 archbishop Sofronios of Cyprus participated in a council in Constantinople which condemned nationalism, triggered by the unilateral declaration of autocephaly by the Bulgarian church.
John Hackett published "A history of the Orthodox Church of Cyprus" in 1901. At about the same time the church went through a crisis regarding the succession of the archbishop. The two candidates, Kyrillos II and Kyrillos III had mainly political differences (one was a nationalist whereas the other was a moderate).
Although the Church gained more freedom under British rule, the British Administration interfered, in certain cases, using restrictive laws on the management of the Church and other areas of national and cultural activity. This led to the October 1931 riot organised by bishops who were also members of the legislative assembly. As a consequence of this uprising, bishops Nikodemos of Kition, and Makarios of Kyrenia were exiled, and restrictions were imposed on the election of the Archbishop. As a result the filling of the Archbishop's throne was pending from 1933 (the death of Archbishop Kyrillos III) to 1946, when the Bishop of Paphos, Leontios, was elected as the new Archbishop.
In 1950, Makarios III was elected Archbishop. While still Bishop of Kition he had demonstrated strong intellectual and national activity. In 1949 he founded the Apostle Varnavas Seminary, and in 1950 he organised the referendum on the Union (Enosis) between Cyprus and Greece. While archbishop he was the political leader of the EOKA liberation struggle in the years 1955-1959. The British exiled him to the Seychelles because of his activities.
In 1960, Archbishop Makarios III was elected President of the newly established Republic of Cyprus. Disagreements of the other three bishops with Makarios lead to the Ecclesiastical coup. Following the dethronement of the Bishops of Paphos, Kitium and Kyrenia for conspiring against Makarios, two new Bishoprics were created: the Bishopric of Limassol which was detached from the Bishopric of Kition, and the Bishopric of Morfou which was detached from the Bishopric of Kyrenia. The Coup d'état of 15 July 1974 forced Archbishop Makarios III to leave the island. He returned in December 1974.
The destruction of Christian monuments was another important consequence. Churches containing Byzantine icons, frescoes and mosaics of incalculable value have been pillaged by antiquities dealers and sold on the black market. One of the most prominent cases of pillage was of the mosaics of Panayia of Kanakaria of the 6th century AC, which were finally returned to the Church of Cyprus, following a ruling by the Indianapolis Court. In the occupied areas of Cyprus there are 514 churches, chapels and monasteries, many of which were converted to mosques, museums or abandoned.
In old age, Archbishop Chrysostomos suffered from Alzheimer's disease and was unable to carry out his duties for a number of years. In May 2006, Ecumenical Patriarch Bartholomew I chaired a broader meeting of church elders which called for Chrysostomos' "honorary removal."
Metropolitan Chrysostomos of Paphos, 65, was elected the new archbishop on November 5, 2006, after a long-running election campaign, becoming Archbishop Chrysostomos II, Archbishop of Nea Justiniana and All Cyprus.
The Holy Synod meets regularly in the first week after Easter and in the first fortnight of the months of February and September. It meets in ad hoc sessions when it is deemed necessary or when two of its members put forward a request.
See also: List of Archbishops of Cyprus