The Church or the new Christian faith established by St. Thomas along  the Southern coast of India composed primarily of Jewish and Brahmin converts. Apart from traditions and liturgies left behind by the Apostle until his martyrdom in AD 72, the fledgling Christian community had no Episcopal setup or Liturgical understanding. The Church then was ruled by prelates of the Sankarapuri and Pakalomattam families. In fact the Church was increasingly getting stagnant until the infusion of fresh Christian blood came to Malankara in the Fourth Century by means of a trader also named Thomas (From Cana) locally known as Kannai Thomman. He brought along with 72 Families whom the Local Rajah gave special grants and who settled among the locals. They established the foundation of Syrian Christian Kerala. This established a relation of the Church in Malabar or Malankara with the East Syrian or Chaldean or The Assyrian Church of the East (formerly officially Nestorian) also believed to have been established by St. Thomas the Apostle in Persia in the First Century. The Church in Malankara was henceforth overlooked by prelates from the Persian Church but was never directly ruled by it. This continued for almost 12 centuries from the fourth to the 16th century when the Portuguese colonized the local Churches.

This Latin connection also brought division to the St.Thomas Christians.   The Coonan Cross Oath in 1653 at the Church of Our Lady of Life at Mattanchery was the culmination of several years of latinization by the Portuguese, and the crowd gathered there took an oath that they would not be subject to the Portuguese Archbishop of Goa, Francis Garcia. 

After the Coonan Cross Oath, Rome began to take an active interest in the Kerala Christians. Several Carmelite monks were sent to Kerala and Carmelite Vicar Apostolics were residing at Varapuzha. Also, the Portuguese nominated administrators or archbishops for Malabar who were stationed at Kodungallur. This dual jurisdiction also was cause for complaints to Rome. In 1787, Representatives from 84 churches assembled in Angamly and drew up a document called Angamaly Padiyola which made a strong demand to Rome for native bishops, citing the sins of omission and commission of the foreign missionaries. In 1861, the arrival of a Chaldean Catholic bishop, Thomas Rokkos sent by the Chaldean patriarch created more problems. He was excommunicated on his arrival by the Vicar apostolic of Varapuzha, and a schism followed. Another Chaldean bishop, Elias Melus arrived in 1874 and he too met the same fate. The Syrian Christians, popularly known as the Surais, in and around Thrissur who owe allegiance to the Syrian Nestorian patriarch are the followers of the schism Melus created.

Today the Church is one of the smallest independent Churches of Kerala with around 100,000 followers and constituting less than 1% of all Christians in Kerala.

Malankara Independent Syrian Church of Thoziyur

In 1772 Mar Gregorios consecrated Abraham Mar Koorilose as bishop. This was not appreciated by his fellow bishop, who hindered his ministry. Mar Koorilose eventually retired to Thoziyur (near Thrissur) where he led a life of prayer. This church continued as an independent church since then. Three time during its life time the main Malankara Syrian Church found themselves without a bishop. The Thoziyur Independent Church provided bishops for it to maintain its apostolic succession. Later it also provided a bishop for the Mar Thoma Church when it found itself without a bishop even though the doctrines of Mar Thoma Church and the Thoziyur Church are different. In return when the Thoziyur Church was without a bishop, the Mar Thoma Church provided a bishop for it. Thus Thoziyur church became an instrument of maintaining the apostolic succession without break within the sister Malankara churches.

Until recently Thoziyur was the only church under this Bishopric. With the increased membership additional churches are being built. Cochin currently has a new church.

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