The Mar Thoma Church is a branch of the pre-16th century undivided Syrian Orthodox Church, 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 in India, Palakunnathu Abraham Malpan (popularly known as Abraham Malpan) in the early part of the 19th Century, and traces its origins to St. Thomas the Apostle who, according to tradition, came to India in AD 52. Protestant missionaries - supported by the English presence in India - encouraged doctrinal, liturgical and ecclesiastical reforms in the Mar Thoma Church. Worldwide, it is the only Eastern rite Church which accepted the Protestant reforms and reformist theology.

The Mar Thoma Church is headed by a Metropolitan bishop who lays claim to the Malankara Throne of St. Thomas. In 2005, the current Metropolitan is His Grace The Most Rev. Dr. Philipose Mar Chrysostom Mar Thoma, who has his throne at Tiruvalla, Pathanamthitta, Kerala, India. He is the 20th Mar Thoma Church Malankara Metropolitan to occupy the Holy Apostolic Throne of St. Thomas after the

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.