According to the sources in the Acts, Saint Paul, Christ's disciple, began spreading Christianity in Hellenic Macedonia and elsewhere on the Balkan Peninsula towards the mid 1st century AD. He visited this region on two occasions during his journeys through Europe and Asia. He was followed by Timothy and Silas, who remained in Macedonia after his departure. At that time, as a Roman province Macedonia often changed its borders and its ethnic composition. As a result of the Christianization in the first three centuries, the Christians in Macedonia at the beginning of the 4th century already had an organised Church with an established ecclesiastical hierarchy, whose bishops regularly participated at the ecumenical councils.
In the 5th century the Church had several metropolises and dioceses. The metropolises of Thessalonica and Scopia were the most distinguished among them. Several Christian basilicas originate from this period, including the one near the village of Bardovci, in the western outskirts of present-day Skopje.
During the reign of the emperor Justinian I (527-565), who came from the village of Tauresium in the Scopia region, a new town was built near the emperor's birthplace, named Justiniana Prima after him. The Metropolitan of Scopie was appointed an autocephalous Archbishop. Cathellian was the first Archbishop of the Archdiocese Justiniana Prima. The other archbishops were: Benenat, Paul, John I, Leon and the last one John IX, who in 680-81 took part at the Trullo Council in Constantinople.
The Slav colonisation of Macedonia began in the 7th century, when the Slavs were assimilated with the native inhabitants. Their Christianization began in the 9th century with the life and work of the holy brothers, Saints Methodius and Cyril, who came from Thessalonica. They first created Glagolithic alphabet then the Cyrillic alphabet and translated the Holy Bible and several other scriptures so that the church services could be held in the vernacular. Their mission was continued by Saints Clement and Nahum of Ochrid at the end of 9th and in the beginning of the 10th century. Saint Clement founded the first University of the Slavs in this region, and Saint Nahum founded the first Slavic monastery on the shore of Lake Ohrid.
In the second half of the 10th century, within the borders of Bulgarian ruler Samuil's state, the autocephalous Ochrid Archdiocese was established with the rank of patriarchate. After the fall of Samuil's state, the Ochrid Archdiocese was reduced to a lower rank of church hierarchy (archbishopric) and it existed as such for eight centuries, until its abolishment in 1767 by the Turkish sultan Mustapha III, and its dioceses were annexed to the Patriarchate of Constantinople. Its dioceses were under several jurisdictions of the neighbouring Orthodox Churches and this struggle became particularly fierce in the second part of the 19th and the first part of the 20th century.
Although the autocephaly enjoyed by Ochrid was claimed by the Bulgarian Orthodox Church, the national movement of Slav Macedonians claimed historical decendance from it. Supported by Roman Catholic Josip Broz Tito's Communist Yugoslav Partizans, right before the end of the war, in 1944, in the village of Gorno Vranovci, an Initiative Board for the Organisation of the Macedonian Orthodox Church was formed. In March, 1945, in Skopje, a Resolution to create a Macedonian Orthodox Church, on the basis of historical continuity with the Archdiocese of Ohrid, was made at the First Clergy and Laity Assembly. This decision was submitted to the Holy Synod of the Serb Orthodox Church who had, since 1919 administered the portion of Macedonia included in 1913 in the Kingdom of Serbia and later Yugoslavia. The move to create a separate Macedonian church in the newly created People's Republic of Macedonia was seen as a a move by the Yugoslav Communist leadership to check the influence of the Serb Orthodox Church and the Serbs in general, the relative majority in Yugoslavia.
The Synod of the Serbian Orthodox Church did not accept this decision which violated canonical law. This resulted in the following actions of the Initiative Board: instead of as an autocephalous, the Board insisted on the Church being recognised as autonomous. This request was also rejected. In 1958, the Second Clergy and Laity Assembly was held in Ohrid and the proposal for restoration of the Ohrid Archdiocese of Saint Clement as a Macedonian Orthodox Church was accepted and Dositheus (Dositej) was appointed the first archbishop.
The Holy Synod of the Serbian Orthodox Church agreed with the decisions of the Macedonian Clergy and Laity Assembly in the resolution AS. No 47/1959 and 6/1959, minutes 57 of June 17/4, 1959 under strong Communist pressure.
As a sign of agreement, a Liturgy was celebrated with the Serbian Patriarch German, on July 19, 1959, in Skopje, in the church of Saint Menas. At the same time, Clement was ordained the bishop of Prespa and Bitola. This meant that the Holy Synod of the Serbian Orthodox Church gave autonomy to the Macedonian Orthodox Church, which remained in canonical unity with the Serbian Church under their Patriarch. Few days later, in the church of St. Nicholas in Štip, H.E. Nahum was ordained the bishop of the diocese of Zletovo and Strumica. The Holy Synod of the Macedonian Orthodox Church was established together with other administrative bodies in the Archdiocese and the dioceses in conformity with the Constitution of the Macedonian Orthodox Church.
In May, 1962, accompanied by Serb Patriarch German and other representatives of the Serbian Orthodox Church, Patriarch Alexis of Moscow visited the Macedonian Orthodox Church. Among them were Metropolitan Nicodemus, Bishop Pimen and other dignitaries of the Russian Orthodox Church. On the feast of Saints Methodius and Cyril, in the church of the Holy Mother of God Kamenska, in Ohrid, Patriarch Alexis of Moscow, Patriarch German and the Macedonian Metropolitan Dositheus concelebrated Holy Liturgy. It was the first Holy Liturgy to be concelebrated by the head of the Macedonian Orthodox Church with heads of other autocephalous Orthodox Churches.
In 1966 the relations with the Serbian Church got worse again. Due to the conflicts and misunderstandings, the Holy Synod of the Macedonian Orthodox Church summoned the Third Clergy and Laity Assembly on July 17, 1967, in Ohrid. At the formal session in the Ohrid church of St. Clement, the Holy Synod proclaimed the Macedonian Orthodox Church as autocephalous. The act of proclamation was made by the Holy Synod of the Macedonian Orthodox Church during the Holy Liturgy celebrated in the church of St. Clement of Ohrid on July 19, 1967, or exactly on the second centennial after it had been banned by the Ottoman authorities. This issue was strongly rejected not only by the Serb Patriarch but also by the Oecumenical Patriarch of Constantinople as being in flagrant violation of canonical law.
The jurisdiction of the Macedonian Orthodox Church spreads not only throughout Macedonia, but also in the church communities abroad.
According to Article 17 from the Proclamation of Autocephaly, the Macedonian Orthodox Church as an administrative part of the One, Holy, Catholic and Apostolic Church is to observe the Holy Scriptures and the Holy tradition, the Canons of the Apostles and the decrees of the ecumenical councils and is to follow them and the Constitution of the Macedonian Orthodox Church.
Since the independence of the Republic of Macedonia from Yugoslavia and the end of Communist repression of the Church, the Serb Orthodox Church has been in conflict with the Macedonian Orthodox Church which yet to gain recognition from the Constantinople or any other autocephalous church. The issue of dispute is the anti-canonical method used to gain autocephaly, the issue of the Serb Orthodox minority in Macedonia (at least 40,000 strong) and the question of some hundreds of Serb Orthodox shrines from the medieval Nemanjic period found in the republic nowadays. The two Churches had been negotiating a compromise reached in Niš in 2002, which would have given the Macedonians de facto independent status (canonical autonomy just as in 1959) but short of canonical autocephaly which was unilateraly proclaimed in 1967. Unfortunately, the agreement was not respected by the Macedonian side save for bishop Jovan who was later arrested and removed from his bishopric as well as expulsed from Macedonia.History of Christianity in Hellenic Macedonia
The Arrival of the Slavs in Macedonia
Samuil's Bulgarian state and the Ochrid Archdiocese
The Macedonian Orthodox Church