
The Thomas Christians who had freed themselves in 1653 from enforced submission under Rome stood for a time together under their leader Mar Thoma, elevated by the community to the status and function of bishop. The Portuguese–Roman Catholics did not accept defeat and tried repeatedly to resubject the Thomas Christians. Those who stood with Mar Thoma, even after a larger section defected to Rome, strengthened their stand as an independent church—the Orthodox Church of India today. From 1663 the Dutch replaced the Portuguese; the Dutch did not persecute the Orthodox but largely ignored them, while the Roman side enjoyed political support.
From 1653 till 1816 the Orthodox Church was led by eight bishops with the common name Mar Thoma. They were indigenous leaders from the Pakalomattam family, archdeacons by heredity and tradition, and “the Gate of All India.” They were deadly against Roman Catholic supremacy and allowed no compromise on church autonomy. Mar Thoma I (1653–1673) fulfilled the Coonen Cross Oath’s aim, sought confirmation of his episcopal office from the West Syrian bishop Mar Gregorios (1665), and thus began a new relationship with West Syrian Christianity that in time made this section Orthodox and part of the Oriental Orthodox family. Mar Thoma I is esteemed as the “greatest soldier” and founder of the Malankara Orthodox Church.
The West Syrian bishops who came from 1665 gradually introduced their church traditions. Mar Thoma V and VI refused to submit to the Patriarch’s jurisdictional claims; when the Patriarch sent bishops in 1751 to reconsecrate Mar Thoma V under the Patriarch with the title Dionysius, he refused. A rival metropolitan was consecrated against him, but Mar Thoma V did not yield. Mar Thoma VI later underwent a confirmation ceremony (1772) and was given the Episcopal title Dionysius—he is known as Dionysius the Great. The residence of the Orthodox bishop moved from Angamaly to Kandanad and later to Kottayam (1816).
The Orthodox were estimated at about 50,000 in the 18th century. By the beginning of the 19th century, Richard Kerr and Claudius Buchanan reported between 30,000 and 80,000 faithful and about 55 churches. Many churches were in decay; some were shared with the Romo-Thomas Christians. Despite divisions, a common community consciousness among the Thomas Christians could not be fully broken—marriages between the sections and shared cultural and church heritage continued.