East Syrian connections were declared heretical by the European missionaries. They alleged that St Thomas Christians believed in Nestorian Heresy as they accepted bishops from the East Syrian Church which officially had accepted Nestorianism. 

As the last Bishop appointed by the East Syrian Patriarch died in 1597 the Portuguese tightened their hold on the Saint Thomas Christians and furthermore didn’t permit any more East Syrian Bishops to enter Malabar. Hierarchically they were brought under the rule of the Latin Bishops after the Synod of Diamper. This officially imposed communion began with Diamper in 1599 and this lasted until Coonan Cross Oath in 1653. In the infamous ‘Coonan Cross Oath’ at Mattancherry, many St. Thomas Christians vowed to disobey the Latin hierarchy. It is interpreted as the independence from colonising intruders. Thus, began a rift among St. Thomas Christians, who were one Church until that time. Eventually, some returned to the jurisdiction of the Latin rule to be in communion with the Pope, while others stood firm in their stand of opposition to the Portuguese. Those who continued under the Latin rule formed the community that became the Syro-Malabar Church. Those who remained opposing the Portuguese encountered the Jacobite Patriarch and eventually became Jacobites, of which a fraction reunited with the Catholic Communion in 1930; they are now known as the Syro-Malankara Church

 

Finally, after 230 years of Latin governance, the Syro-Malabar Church hierarchy was established in India, in 1923. Since then it has grown rapidly, and in 1992 Pope John Paul ll elevated it to the status of a Major Archiepiscopal sui iuris Church with the title of Ernakulam-Angamaly. It is one of the four Major Archiepiscopal Churches, the other three being the Syro-Malankara Church, Ukrainian Church and the Romanian Church.