The name of Rhodes is mentioned in the New Testament (Acts. 25, 1), at the time of Paul's return to Jerusalem, during the third apostolic tour. Paul is considered to be the founder of the Church of Rhodes, while religious tradition holds that the Apostle Silas, the companion of the Apostle of Nations, preached and performed miracles on Rhodes.

It is not known when Rhodes first became a Diocese. According to tradition, Prochoros is mentioned as its first Bishop during the First Century. Bishop Efranor was mentioned during the Second Century, and Bishop Foteinos was mentioned during the second half of the third century, at the time of the martyrdom of the Holy Martyrs Clemes and Agathaggelos. Bishop Euphrosynos took part in the First Ecumenical Council.

According to the political geography of the Byzantine Empire, Rhodes was the Metropolis of the Province of the Islands.

The Province of the islands was the twenty-ninth in order and included the following cities: Rhodes, Kos, Samos, Chios, Mytilene, Methymna, Petelos, Tenedos, Proselini, Andros, Tinos, Naxos, Paros, Sifnos, Milos, Ios, Thira, Amolgos and Astypalea.

In ecclesiastical geography, the Diocese of Rhodes was promoted to a Metropolis around the late fourth or early fifth century, since in the earliest known "order of seniority" it is listed as 26th among the Metropoles of the Throne.

The changes in the "order" of the Metropolis of Rhodes in the following centuries are: As of the Council of Chalcedon (451) it became 28th. Since the mid-sixth century until the early seventh, it held the 33rd place and it had eleven Dioceses. From the middle of the eighth century it held the 33rd place, at the beginning of the ninth the 30th place, during the tenth and up to the beginning of the twelfth century the 38th place, at the end of the thirteenth and the beginning of the fourteenth century the 45th, while during the seventeenth century it receded to the 38th place with only one Diocese, that of Lerni.

As regards the number of Dioceses that were under the jurisdiction and spiritual guidance of the Metropolitan of Rhodes, we note the following: From the beginning of the seventh century and until the beginning of the ninth, the Metropolitan of Rhodes had 11 Dioceses under his care. Around the middle of the ninth century they grew to thirteen, with the establishment of the Dioceses of Nisyros and Astypalea. At the beginning of the tenth century they decreased to ten, with the abolishment of the Dioceses of Nisyros and Astypalea and the annexation of the Diocese of Andros to the Metropolis of Athens. In the middle of the same century they again rose to thirteen, because the Dioceses of Nisyros and Astypalea reappeared and the Diocese of Ikaria was added. Between the years 971-972 they were once more reduced to ten, because the above three Dioceses were not registered. Between the years 972-976, the three Dioceses reappeared and the Diocese of Tracheia was added. Later on the Dioceses amounted to 15, after the appearance of the Bishops of Linos and Apameia as annexed to the Metropolis of Rhodes (Taktikon of the seventeenth century).

The Metropolis of Rhodes flourished at the period until the conquest of Rhodes by the Knights of the order of St John. Its Bishops participated in the Ecumenical Councils: Ellanikos or Ellanodikos in the third, Theodosios in the fifth, Isidoros in the sixth and Leon in the seventh.

During the Hospitaller period, the Metropolis of Rhodes entered a critical period. The Metropolitan of Rhodes was expelled and a Latin Archbishop assumed his place. The church property was looted. The Ecumenical Patriarchate continued to ordain Metropolitans of Rhodes, who stayed away from their Metropolis, since the Latins did not allow them to assume their position. In 1369 the administration of the Metropolis was entrusted to the Metropolitan of Sidi "par excellence". All this time the administration of the Metropolis was exercised by a board consisting of higher-order clerics and elders of the island.

A limited change in the situation occurred in the middle of the fifteenth century, due to the fall of Constantinople and the threat of a Turkish invasion. Notably, the Latins aven allowed an Orthodox Metropolitan to assume his position. The Metropolitan of Rhodes, Nathanael, attended the Council of Florence, but when he returned to his seat, the Latin Archbishop did not allow him to disembark. The reaction of the people to the "union" achieved in the Council of Florence was strong and the Latins used violent repressive measures against the Orthodox population.

In 1522, Rhodes was conquered by the Turks. The first Metropolitan who assumed office was Efthimios, who was subsequently hanged as the instigator of a revolutionary movement. The church life during the Ottoman occupation was characterized by relative tranquility, although there was no lack of problems caused by the arbitrariness of the conquerors. During the years of the Revolution and the years that followed it, the Church suffered persecution and its privileges were abolished. The firman of Sultan Mahmud the Second in 1835 reinstated these privileges, which were abolished anew during the time of Neoturkish government.

In 1912 Rhodes, like the rest of the Dodecanese was taken by the Italians, who in the beginning showed respect for the Church. Subsequently they changed moods, abolished all privileges, followed an oppressive policy and created the so-called issue of 'autokephalon' (i.e. self-governing and independent church) status, which rocked the local community. The burden of shepherding the Metropolis of Rhodes throughout the Italian occupation was borne by the Metropolitan Apostolos Tryphonos, who was forced to resign on 8 June 1946. After the incorporation of the Dodecanese into Greece, the Metropolis of Rhodes entered its modern period of history. The islands of Symi, Halki, Tilos and Kastellorizo were detached from it in 2004, to establish the Diocese of Symi, while Nisyros was annexed to the Metropolis of Koou.