The Diocese of Kottayam was erected exclusively for the Southist (Knanaya) Catholics in 1911.
The Knanaya Community traces its origin from a group of Jewish-Christian emigrants from Southern Mesopotamia to the South Indian port of Cranganore in A D 345, who formed themselves into an endogamous community. They co-existed peacefully in the Indian nation and fulfilled their missionary purpose of re-invigorating the Church of St. Thomas Christians. The original community consisted of about 400 persons belonging to 72 families of seven septs headed by Thomas of Kynai. A bishop by name Uraha Mar Yousef, four priests and several deacons were among them.
As the Catholicos of the East had promised the emigrants that he would send from time to time bishops to India, Uraha Mar Yousef had successors till the end of the 16th century. Under the East Syrian Bishops, the Knanaya Community had their own churches and priests distinct from those of the non-Knanaya St. Thomas Christians. This system continued also under the Latin Rite European bishops, who governed the St Thomas Christians. When a ritual separation was effected for the Catholics in Kerala between the Orientals and Latins in 1887, all the Knanaya Catholics de facto were in the Apostolic Vicariate of Kottayam, and the Holy See ordered Bishop Charles Lavigne to appoint a separate Vicar General for the Knanaya Community. When the Vicariates Apostolic were re-organized into Trichur, Ernakulam and Changanassery and three indigenous bishops were appointed for the Syro-Malabarians in 1896 the bishop appointed for the Vicariate of Changanassery was Mar Mathew Makil, the former Vicar General for the Knanaya Community.
On August 29, 1911 the Vicariate Apostolic of Kottayam was re-constituted exclusively for the Knanaya Community by the Apostolic letter "In Universi Christiani" of His Holiness Pope St Pius X.
On December 21, 1923 the Vicariate Apostolic of Kottayam was raised to an Eparchy by Pope Pius XI. When the territorial limits of the Syro-Malabar Church was extended in 1955, the jurisdiction of the Eparchy