The history of the Mar Thoma Church is divided into three main eras viz.

1. Pre-Reformation
2. Reformation
3. Post Reformation.

Pre - Reformation Era
St. Thomas, the Apostle of Jesus Christ is believed to have landed in AD 52 in Cranganore near Cochin , which was at that time an important seaport on the Malabar Coast, having trade connections with the Middle East in those days. F.E. Keay in his book, A History of the Syrian Church in India has established, from the mention in the book of Kings, of the articles brought to the court of King Solomon from India , that even before the time of Christ, there was trade between the Malabar Coast and Palestine in spices and luxury articles like ivory. Therefore, it was quite natural for Thomas to come to India with the Gospel as the disciples went to different parts of the world in accordance with the commission given to them by Jesus Christ. In the true Apostolic tradition he preached first to the Jewish settlers in and around Cochin , and then worked among the Hindus. Through the ministry of the Word and the many miracles which tradition attributes to him, he brought many high caste Hindus to the Christian faith. It is believed that he organized 7 Christians communities for the use of these Christians, and ordained presbyters from four leading families. The seven churches were, 1. Cranganore (Malankara) 2. Chavakad (Palur) 3. Parur near Alwaye 4. Gokamangalam, 5. Niranam 6. Nilakkal (Chayal) and 7. Quilon (Kalyan). All these places except Nilakkal are near the sea coast. Nilakkal is in the ghat region near Sabarimala, the Hindu place of pilgrimage. It is believed that Nilakkal was an important trading centre for export of spices and other items like ivory, and the route extended to Tamil Nadu across the ghats. Remains of ancient human dwellings and places of worship are still discernible among the ruins in this area, which is now covered with forests. Many Christian families in Kanjirappally, Ayroor and other places trace their origin to Nilakkal. There is a Mar Thoma Church at Ayroor which is still named Chayal (Nilakkal). Recently a new Church has been built under the joint auspices of all the Christian denominations of Kerala at the site agreed upon by all concerned. This Church has having historical significance as the first Church built and dedicated by all the denominations together as a symbol of the heritage from St Thomas . It is believed that St. Thomas proceeded to the East coast of India and died a martyr’s death at a place called St. Thomas Mount, and was buried at Mylapore in Madras .

Dr. Juhanon Mar Thoma Metropolitan concludes the Chapter on the St Thomas Tradition in his book Christianity in India and a Brief History of the Mar Thoma Church as follows: “The History of the Christian Church in the first century does not depend entirely on historical documents. Tradition is often more true and more compelling than plain historic proof. In this sense St Peters founding of the Roman Church and St Thomas founding of the Malabar Church , may be said to stand on the same footing.