The Portuguese Admiral Vasco da Gama arrived in Calicut on 20 May 1498. When Gama and the Portuguese missionaries arrived they found no Christians in the country except in Malabar Coast (modern day Kerala). The Christians they found were St. Thomas Christians. The Christians were friendly to Portuguese missionaries at first; there were exchange of gifts between them, and these groups were delighted at their common faith.
Later, due to certain differences, mainly in the liturgy, the relations between the missionaries and local St. Thomas Christians became increasingly strained. Under the Padroado (patronage) agreement with the Holy See the Portuguese missionaries started to interfere in day-to-day operations of the church and things took a turn for the worse. They accused the Indian Christians of heresy and schism (also see: Schism in Christianity); and attempted to introduce the Latin customs and Latin manner of ecclesiastical administration, severing the East Syrian connection.
The Portuguese established a Roman Catholic (Latin Church) diocese in Goa (1534) and another in Cochin (1558) with the hope of bringing the St. Thomas Christians under Latin Catholic jurisdiction. At a Goan Synod held in 1585, it was decided to introduce the Latin liturgy and practices among the Thomas Christians. During the Synod of Diamper of 1599, the Portuguese Archbishop, Don Alexis Menezes, succeeded in appointing a Latin bishop to govern the St. Thomas Christians. The Portuguese padroado (patronage) was extended over them. The strife between the Portuguese missionaries and the indigenous Christians and their Mesopotamian prelates was of an ecclesiological and jurisdictional character. Attempts to resist the Latinization process were branded as heretical. Under their Archdeacon, the Thomas Christians resisted, and, consequently, the once united Church in full communion with the East Syrian Patriarch ended up in various denominations