The Malankara Mar Thoma Syrian Church, commonly referred to as the Mar Thoma Church is a Reformed offshoot of the pre-16th century undivided Saint Thomas Christians, and got its current identity in 1889, even though it was born much earlier. It has its roots in a reformist movement started by a teacher-priest of the Syrian Orthodox Church, Palakunnathu Abraham Malpan (popularly known as Abraham Malpan) in the early part of the 19th Century. It is one of several groups of Saint Thomas Christians tracing their origins to St. Thomas the Apostle who,according to tradition, came to India in AD 52. Anglican missionaries - supported by the English colonial rule in India - encouraged doctrinal, liturgical and ecclesiastical reforms in the Church which were viewed as heretical by Syrian Orthodox bishops.
The reformists broke from the Syrian Orthodox Church when they were excommunicated for refusing to recant their changes. Prior to 1996, it was the only Eastern rite Church worldwide which inculcated elements of Protestant thinking and reformist theology (the Ukrainian Lutheran Church was established in Ukraine after the fall of the Soviet Union).

The Mar Thoma Church is headed by a Metropolitan bishop who lays claim to the Malankara Throne of St. Thomas.
The current Metropolitan is His Grace The Most Rev. Dr. Philipose Mar Chrysostom Mar Thoma, who has his throne at Tiruvalla, Pathanamthitta District, Kerala, India. He is the 20th Malankara Metropolitan to occupy the Holy Apostolic Throne of St. Thomas after the re-establishment of the episcopacy in the 17th century. The majority of the membership of the church is in the southern Indian state of Kerala but it has spread with the 20th Century Indian diaspora to North America, Europe, the Middle East, Malaysia, Singapore, South Africa, Australia and New Zealand, this in addition to a sizeable population in the rest of India.The Mar Thoma Church is in full communion with the Anglican Church, Church of South India and Church of North India.