The Mar Thoma Christians were one of many extensions of the
Church of the East. This church had also reached
China by the 7th century, it had a very successful missions in the early centuries of Christianity, but suffered greatly after the Muslims, and then to some extent from the Mongols (although the church had Christianized some members of the leading Mongol families).
The coast of south India (
Kerala today) escaped both of these later catastrophes. It was along a major
trade route from the Roman empire, and there were already Jews living there at the time of Christ. In fact the Jewish community may have predated the Roman conquest of Syria and Palestine. Apparently these people were primarily engaged in the spice trade.
It was a natural development for Christianity to follow this path, as it usually progressed along the trail of synagogs in the beginning of Christian history.
There are two Thomases involved in the story of this community. The first is the Saint Thomas of Biblical fame, who supposedly went to India as his own mission. Highly mythologized accounts appear in apocryphal literature.
The second Thomas was Saint Knai Thoma, who with Mar Joseph led a colonial expedition of Jewish Christians from Mesopotamia to India a few centuries later.
There is also still an endogamous community of Jewish Christians in Kerala (Knanaya Christians), but most of the Mar Thoma Christians there are not endogamous.
The Mar Thoma Christians were a unified people associated with the Church of the East until the Portuguese arrived. The connection with their mother church was forcibly severed by the Portuguese, who prevented bishops from coming to serve their people.