St. Thomas, one among the twelve apostles arrived In Kodungalloor ( Old name Muziris ) in Kerala in 52AD and established seven churches. He was matyred in Mylapore ( Chennai ) in 72AD. The seven churches he established are in  Ezharapallikal: Kodungallur, Kollam, Niranam, Nilackal (Chayal), Kokkamangalam, Kottakkayal (Paravoor), Palayoor (Chattukulangara) and Thiruvithancode Arappally – a “half church”.

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An organised Christian presence in India dates to the arrival of East Syrian settlers and missionaries from Persia, members of the Church of the East or Nestorian Church, in around the 3rd century. Saint Thomas Christians trace the further growth of their community to the arrival of the Nestorian Thomas of Cana from the Middle East, which is said to have occurred sometime between the 4th and 8th century. The subgroup of the Saint Thomas Christians known as the Knanaya or Southists trace their lineage to Thomas of Cana, while the group known as the Northists claim descent from Thomas the Apostle’s indigenous converts; some additionally assert ancestry from Thomas of Cana through a second, Indian wife.

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Original Assyrian Church has split into two different traditions in the form of rivalling doctrinal loyalties: East Syrian (Nestorian) and West Syrian (Jacobite, named after Jacob Baradaeus, died 578). The doctrinal division was highlighted by linguistic distinction in the form of different dialects and distinct Syriac scripts. The doctrinal difference centered on the divine and human nature of Jesus Christ.Presently, the Syriac-speaking churches survive under the following in Kerala.

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 Syro-Malabar of India

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1. Syrian Orthodox of the Patriarchate of Antioch including its Church in India

2. Syrian Orthodox of the Autocephalous (meaning independent) Malankara

Church of India

3. Syrian Catholic

5. Malankara Catholic of India

6. The Church of Mar Thoma, a church of India that broke off from the Syrian

Orthodox Church and blended Eastern Orthodoxy with Anglicanism.

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Indian Kings always supported and helped the Christian missionaries and Christian settlers to continue with their religious work and conversions. The religious tolerance of Indians enabled Jews , Parsis and Christians flourish in India and escape persecution from other parts of the world . The  Portuguese of Roman Catholic faith were the first in India to persecute Christians in India .

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Europeans discovered the Christians of India when the Portuguese arrived in Southern India on May 20, 1498. The Portuguese quickly decided that the Saint Thomas Christians were heretics. As early as 1543, Francis Xavier and other clerics advocated the setting up of the Holy Office of the Inquisition to deal with the Nestorians and the Jews in India. It was established in India in 1560.

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For 55 years the Christians of Southern India endured persecution from the Roman Catholic Church. Indian priests were arrested and put through the inquisition and some were executed. Harassment of Nestorian Christians began in 1558. On 26 June 1599 at the Synod of Diamper the St. Thomas Christians were coerced to join the Roman Catholic Church and to conform to European practices. The Roman Catholics gathered all the Syriac books they could find and put them to the torch. Records of centuries of Assyrian church history in India and perhaps additional accounts of the work of Saint Thomas in India were lost forever. The Portuguese forced the Saint Thomas Christians to profess themselves to be Roman Catholics. The Christians of India resented the arrogance and intolerance of their European oppressors. When a Syrian Orthodox priest arrived in India, all the Saint Thomas Christians rallied to him. They all adhered to the Syrian Orthodox Church and renounced Roman Catholicism.

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The Malankara Church is the church of the Saint Thomas Christians of Kerala, India, with particular emphasis on the part of the community that joined Archdeacon Mar Thoma in swearing to resist the authority of the Portuguese Padroado in 1653. This faction soon entered into a relationship with the Syriac Orthodox Church of Antioch, and was thereafter often known as the Malankara Syrian Church (Malayam: Malankara Suriyani Sabha).As an independent faction, it originated in the first major split within the Saint Thomas Christian community. Historically, the Thomas Christians had been united in leadership and liturgy, and were part of the Church of the East, based in Persia. However, the collapse of the Church of the East’s hierarchy in Asia left the province of India effectively isolated, and through the 16th century, the Portuguese, recently established in Goa, forcefully drew the Thomas Christians into Latin Rite Catholicism. Resentment of these measures led the majority of the community to join the archdeacon, Thoma, in swearing never to submit to the Portuguese in the Coonan Cross Oath. Several months later Thoma was ordained as the first indigenous Metropolitan of Malankara.

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Following the Oath, in 1661 Pope Alexander VII established a new East Syrian Rite hierarchy in communion with Rome for the Saint Thomas Christians; by the next year 84 of the 116 communities had joined, forming what is now the Syro-Malabar Catholic Church. The remaining 32 communities stayed independent, and formed a relationship with the Syriac Orthodox Church. Over the next centuries this relationship strengthened, and the Malankara Church adopted a variant of the West Syrian Rite known as the Malankara Rite (as opposed to the previous East Syrian usage) and entered into full communion with the Syriac Orthodox Patriarch of Antioch. However, through this time the church experienced a series of splits, resulting in large numbers of followers breaking away.

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In the 20th century a dispute over authority between supporters of the Metropolitan and supporters of the Patriarch finally divided the church, with the former group becoming the essentially independent Malankara Orthodox Syrian Church and the latter maintaining ties with the Patriarch as the Jacobite Syrian Christian Church. Motions by church leaders and two Supreme Court decisions in the 20th century failed to heal the rift. Other groups to split from the main body are the Malabar Independent Syrian Church, which broke away in 1772; the Malankara Mar Thoma Syrian Church, (also known as Mar Thoma Church) which entered into communion with the Anglican Communion; and the Syro-Malankara Catholic Church, which entered into communion with the Catholic Church as an Eastern Catholic Church with its own liturgy.