Patriarch Peter III was not satisfied with the Court judgment. He was keen to establish that he had full authority over the Malankara Church both in its spiritual and in its temporal matters and not merely an over all spiritual supervision. In fact he protested though nobody responsible in the matter took note of it. His second successor Patriarch Mar Abdullah II was determined to follow up the matter. With this intention he came to Kerala in 1909 and pressed the issue. But that led to a sad division in the Church from 1911, one party siding with the Patriarch and. the other lining up with Metropolitan Mar Dionysius VI of Vattasseril who stood against him and wanted to keep up the independence of Malankara Church.

 From the inception of Church in India, it was having its own Bishops who were having all spiritual powers and Archdeacons who were having all temporal powers, who were controlling the Church. In the sixteenth century Archdeacon was consecrated as Marthoma Merton, and in the nineteenth century changed to the title of Malankara metropolitan with the support of British rulers.

 All that led to a sad division in the Church, from 1911, one party siding with the Patriarch (Jacobites) and the other (Orthodox) lining up with Metropolitan Mar Dionysius VI of Vattasseril who stood against him and wanted to keep up the independence of Malankara Church.

 In July 1909, Dionysius V died and Vattasseril Mar Dionysius ( Dionysius VI ) became Malankara Metropolitan. The Association managing Committee met under the chairmanship of Dionysius VI and elected Murimattathil Poulose Mar Ivanios of Kandanad Diocese and requested the Patriarch Mar Abdul messiah to consecrate him as the Catholicos of the East. Accordingly, on 15th September, 1912, Poulose Mar Ivanios was consecrated as the first Catholicos of Malankara Orthodox Syrian Church with the title of Mar Baselios Poulose I at the Apostolic Throne of St. Thomas.

 In this conflict the Metropolitan could obtain the support of Patriarch Mar Abdul Messiah the immediate successor to Patriarch Peter III. Patriarch Peter III was succeeded in 1895 by Mar Abdul Messiah. By a state interference he had lost his position in Turkey and came to be replaced by Mar Abdullah. While Metropolitan Mar Dionysius VI clashed with Mar Abdullah, the Canonical senior Patriarch Abdul Messiah offered to come to the assistance of the former. Thus in 1912 he came to Kerala and associated with Mar Dionysius VI and the Bishops and the Church with him, to establish the Catholicate of the East in Malankara. The ceremony was held at St. Mary's Church, Niranam on 15 September 1912; Niranam Church is one of the seven Churches founded by St. Thomas during his visit here in the first century. 

 The Catholicate of the East was thus established in Malankara, with the cooperation of the canonical Patriarch Abdul Messiah, who was senior to Mar Abdullah. Thereby the Patriarch himself has withdrawn his right of spiritual oversight if any in the Indian Church, which the Royal Court of Appeal had acknowledged for him in 1889. consecration of the first Indian CATHOLICOS--Moran Mar Baselios Poulose in Apostolic succession to St. Thomas, with the personal participation of Patriarch Abdul Messiah of Antioch

 The designation "CATHOLICOS of the East' to the successors of St. Thomas the Apostle was given by the Jerusalem Synod of AD 231. The head quarters of the Orthodox Church of the East was first at Uraha (Edessa) in Persia. This was moved to 'Seleucia' and it was there the title 'CATHOLICOS of the East' originated. CATHOLICOS is an ecclesiastical dignitary recognized in the Antiochene Syrian Church also. He is equal in rank with the Patriarch though the latter is considered as first among equals (primus inter parees).

 Their names are testament to the Church's eastern connection. The first CATHOLICOS was Baselios Poulose I (September 14, 1912 to May 2, 1913) The second was Baselios Geeverghese I. (April 30, 1925 to December 17, 1928).

 During the time of the third CATHOLICOS (Baselios Geeverghese II ( Feb 15, 1929 to January 3, 1964), the positions of 'Malankara Metran' (Head Bishop) and CATHOLICOS were combined. The fourth CATHOLICOS was Baselios Ougen I (May 12, 1964 to December 8, 1975) and the fifth Baselios Thomas Mathews I (October 27, 1975 to April 27, 1991).When Mar Mathews Baselios I retired, the sixth CATHOLICOS Baselios Mar Thoma Mathews II took office on April 29, 1991.