The Malabar Independent Syrian Church is the oldest of the various jurisdictions into which the non-Roman Catholic section of the Thomas Christians has been divided since the 17th cent. Following the imposition of Portuguese control and European bishops after the Synod of Diamper in 1599, there was an attempt by the whole community to break free of Jesuit control in 1653 at the Coonan Cross incident. Subsequently, as a result of the successful efforts of Carmelite missionaries, the majority of St. Thomas Christians returned to Roman obedience (see Malabar Catholic Church). The remaining section (called Puthenkuttukar or New Party to distinguish them from the Romo-Syrians who were Pazhayakuttukar or Old Party), continued to use latinized E.-Syr. rites, but began to come under the influence of periodic visitors of the Syr. Orth. tradition.

A definitive step took place in 1751 when the Syr. Orth. Mafryono Basilios Shakrallah arrived in Kerala, accompanied by Mar Gregorios of Jerusalem and another companion, whom the Mafryono soon consecrated with the title ‘Mar Ivanios, bp. of India’. The party seems to represent a more systematic attempt to introduce W.-Syr. usage than had been the case with earlier visitors. The delegation was also authorised by the patr. to regularize the orders of the Indian head of the Puthenkuttukar community, Mar Thoma V, with the expectation that he would minister under the jurisdiction of the Mafryono and his companions. Squabbles about money and jurisdiction prevented this intended outcome, and Mar Thoma V died in about 1765, without having been re-consecrated, but having himself consecrated his nephew as Mar Thoma VI.

The Mafryono gathered a small household, among whom he disseminated Syr. Orth. usage. Immediately prior to his death in 1764, he consecrated a native priest of the Kattumangat family as bp., giving him the title of Mar Koorilose. For several years the new bp. lived quietly in a monastic community at Thevanal. In 1770 Mar Gregorios and Mar Ivanios consecrated Mar Thoma VI as Mar Dionysios I. Mar Gregorios seems to have very soon regretted this action and in 1772 raised Mar Koorilose to the rank of Metropolitan. Mar Koorilose also received a ring from the Rajah of Cochin, the traditional acknowledgement of the head of the St. Thomas Christians. Mar Dionysios managed to imprison his rival, who eventually escaped and fled to the village of Anjur in the territory of the Zamorin of Calicut, later British Malabar. A gift of land from a prominent Muslim, whose son Mar Koorilose had healed, enabled a Cathedral Church to be built at nearby Thozhiyur.

Following the failure of validly consecrated bishops among Mar Dionysios I’s successors in the early 19th cent., recourse was had to a successor of Mar Koorilose at Thozhiyur, Mar Philoxenos II, who consecrated three bishops as Malankara Metropolitan (Pulikottil Mar Dionysios II ca. 1813; Punnathra Mar Dionysios III in 1816; Cheppat Mar Dionysios IV in 1825) and who himself occupied that position for several years.

Important legal rulings in the 1850s established the independence of the Thozhiyur Church from either the patr. of Antioch or the Malankara Metropolitan.

In 1894 the two Thozhiyur bishops (Mar Athanasios I and Mar Koorilose V) consecrated a Metropolitan for that section of the Puthenkuttukar which repudiated Patriarchal authority and desired a degree of reform (see Mar Thoma Syrian Church).

The community has always been Syr. Orth. in rite. It has about 15 churches and priests, and several schools. The Church is active in ecumenical activities in Kerala and outside India. In 1998 and 2008 the Metropolitans were Ecumenical Observers at the Lambeth Conference of Anglican bishops. In 2006 both current bishops (Mar Koorilose IX and Mar Basilios I) participated in the consecration of bishops for the Free Church of England.

A Constitution was drawn up in 1947, appointing a Sabha Mandalam, representing all the churches, for special business such as electing a bp., and Council of Clergy and Laity to assist the Metropolitan in governing the Church.

Since the 1970s worship has been celebrated mainly in Malayalam, though Syriac is still used for the Daily Offices and midweek Qurbanas at Thozhiyur Cathedral.