
Following the Synod of Mulanthuruthy and the Royal Court judgement of 1889, the Orthodox were in a divided condition: the reform party formed the Mar Thoma Syrian Church; those who adhered to the Patriarch and West Syrian traditions formed the Jacobite (Orthodox) Syrian Church. Disputes over the exercise of Patriarchal authority led to further division in the 20th century into Orthodox and Jacobites. The Orthodox section established the office of the Catholicos, declaring that the Patriarch possesses only spiritual authority over them while in temporal and administrative matters they are free. In 1934 the Orthodox framed a constitution and united the office of Malankara Metropolitan with that of the Catholicos. Litigations from 1913 to 1958 ended in favour of the Orthodox; a truce was reached in 1958. From 1972 the patriarchal side resumed conflict; Supreme Court verdicts from 1995 onward have not produced a full amicable solution, and the two sections continue—one under the Patriarch and one under the Catholicos.
After the death of Dionysius V, his successor Dionysius VI (Vattasseril Dionysius the Great) became Malankara Metropolitan. Patriarch Abdulla II visited Kerala and sought to stabilize patriarchal jurisdiction over the Indian Church. The Association at Kottayam (November 1909) rejected his demand for a registered deed and for consecrating bishops. The Patriarch excommunicated Dionysius VI (June 1911). Dionysius and his adherents decided to establish the Catholicate to defend the independence of the Indian Church. Abdul Messiah, the predecessor of Abdulla II, was invited; he came to Kerala and established the Catholicate in September 1912. The Orthodox division declared their freedom. The first Catholicos was Moran Mar Baselios Paulose I (1912–14); subsequent Catholicoses were elevated by the Synod of the Indian Orthodox bishops, showing the autocephalous and autonomous status of the Indian Church. The Catholicate now represents the supreme head of the Malankara Orthodox Syrian Church, independent in church administration.
Catholicos Geevarghese II (1929–64) served for 35 years. During his time the Church introduced a constitution, won the final legal victory in 1958, and associated with the World Council of Churches. In 1962 the headquarters of the Catholicos was shifted to Devalokam, Kottayam. Catholicos Augen I (1964–75) was a great Malayalam and Syriac scholar. From August 1974 all relation with the Patriarch broke down again over the Patriarch’s denial of the Throne of St. Thomas and the autonomy of the Church under the Catholicos. The Orthodox section of the Church continues as the Malankara Orthodox Syrian Church—independent and autonomous under the Catholicos.