The Malankara Catholic Eparchy of Bathery is the fruit of the missionary zeal and desire for the unity of the Church expressed by the committed laity, priests and prelates of the Syro-Malankara Church. In 1958, the Holy See extended the jurisdiction of the Eparchy of Tiruvalla further towards the North of Kerala and some districts of Karnataka and Tamilnadu. After the extension His Excellency late Zacharias Mar Athanasios sent priests to the new regions. These pioneers of Malabar mission began to work zealously among the Malankara faithful and they gave leadership for the Re-union movement and Evangelization. As a result parishes and mission centers were established in different places. In order to accelerate the re-union movement and evangelization, His Excecellency Most Rev. Zacharias Mar Athanasios requested the Holy See to bifurcate the Diocese of Thiruvalla and to erect a new Diocese with Sulthan Bathery as its headquarters. His Holiness Pope John Paul II erected the Eparchy of Bathery on 28 October 1978 and Rev. Dr. Cyril Malancheruvil was appointed as the first Bishop of Bathery.
       His Excellency Most Rev. Cyril Mar Baselios officially took charge of the Eparchy of Bathery on 2 Ferbruary 1979 and the new diocese was inaugurated during the solemn function held at St. Thomas Pro-Cathedral, Sulthan Bathery. There were arround 8500 Malankara Catholic faithful in 43 parishes and mission stations at the beginning of the diocese. The pastoral care of the community was entrusted to 18 diocesan priests and 2 priests from Bethany Ashram who were zealous and committed in the Apostolate. Bethany sisters and sisters of Deena Sevana Sabha also gave valuable services in different parts of the diocese. As a result, thousands of families and some priests from prominent families came into full communion of the Catholic Church. Within a short period of time, many parishes and mission stations were established in different parts of the Eparchy.
         Most Rev. Cyril Mar Baselios gave great leadership for all the pastoral activities. The far-sighted vision of Mar Baselios led the Eparchy in the hights of its growth. The Apostolate of the Eparchy was organized under various departments. The faith formation of the children, youth, men and women were guaranteed by the Apostolate of Catechism, youth ministry, ‘Pithrusangam’ and ‘Mathrujyothis’. The Bible Apostolate Department takes initiative for the promotion of Bible studies and distribution of Bible among the faithful. Malankara Catholic Association is the official organization of the Malankara Catholic faithful for the Social involvement and leadership. The Eparchy also gave due importance to its social commitment, taking seriously the life situation of the people around. The Eparchy chalked out a social programme aimed at promoting the integral growth of men and Women. The Social Service Centre, named Shreyas, which is the official organ of the Eparchy for promoting Social justice and fellowship, is instituted in view of creating a more human and just society, based on Gospel values, through a scientific programme of mass education, mass mobilization and mass action. The Eparchy also started few educational institutions under the Corporate Educational Agency of the Eparchy to impart a value based education to the youth irrespective of caste and creed.
         Msgr.Mathew Nedungatt and Msgr.Thomas Thannickakuzhy, Msgr. Thomas Charivupurayidom and Msgr. Eldho Puthenkandathil served the Eparchy as its Vicar Generals. The Diamond Jubilee of the Malankara Reunion Movement was celebrated in the Eparchy on 20, 21 September 1990 at Sulthan Bathery.
         His Eminence Wladislao Cardinal Rubin, the former Prefect of the Congregation for the Oriental Churches visited the Eparchy on 9 January 1981 and inaugurated the Pastoral Council and Parish Senate in the Diocese.
         The Eparchy of Bathery was blessed by the .visit of His Eminence Simon D. Cardinal Lourdusamy, the then Prefect of the Congregation for the Oriental Churches on 25 August 1987.
         After 17 years of inspiring leadership in the Diocese, His Excellency Most Rev. Cyril Mar Baselios left for Trivandrum on 12 December 1995 as he was appointed Metropolitan Archbishop of Trivandrum and the Head of the Malankara Catholic Church. His Grace Cyril Mar Baselios took charge of the Church and of the Archdiocese of Trivandrum on 14 December 1995. From 14 December 1995 till 5 February 1997, the Eparchy was led by Rev. Msgr. ThomasThannickakuzhy as its Administrator. On 18 December 1996 His Holiness pope John Paul ll appointed Very Rev. Dr. Varghese Ottathengil, the then Rector of St.Mary’s Malankara Major Seminary, Trivandrum as the new Bishop of Bathery, Msgr.Varghese Ottathengil was consecrated as Bishop on 5 February 1997 at Mar Athanasios Nagar, Bathery  by His Grace Cyril Mar Baselios, the Head of the Malankara Catholic Church.
         Rev. Dr. lsaac Thottunkal was the Vicar general of the Eparchy from 1999 to 2001. Then he was appointed Apostolic Visitor for North America & Europe and Auxiliary Bishop of the Archieparchy of Trivandrum, on 18 June 2001. His Excellency Rt. Rev. Msgr. lsaac Mar Cleemis was consecrated as bishop on 15 August 2001 at St. Mary’s Malankara Catholic Church, Thirumoolapuram, Thiruvalla.
         The Eparchy of Bathery celebrated its Silver Jubilee year from 28 October 2002 to 28 October 2003. The SilverJubilee celebrations began with the Holy Qurbono by His Grace Most Rev. Dr.Cyril Mar Baselios, the first Bishop of Bathery and with the solemn declaration of the Jubilee year by His Excellency Most Rev Dr.Geevarghese Mar Divannasios On 28 October at St.Thomas Cathedral, Bathery. The concluding celebration of the Jubilee year was held along with the 73rd Re-union celebration of the Malankara Catholic Church on 18 to 20 September 2003.
         During the past years, the Eparchy of the Bathery and its pastoral leadership was formly established in the different geographical area of the Eparchy.  As a result many parishes and mission stations together with social, charitable and educational institutions were established to the Karnataka region of the Eparchy. A new Eparchy for the Karnataka  region was a long cherished dream of the Malankara Catholic faithful in the region. This dream was fulfilled at the moment of the solemn declaration of the new Eparchy of Puttur on 25 January 2010.
         On 25 January 2010, as per the decision of the Holy Episcopal Synod of the Syro-Malankara Catholic Church, and having consulted the Apostolic See of Rome, His Beatitude Moran Mor Baselios Cleemis Major Archbishop-Catholicos, erected the Eparchy of Puttur bifurcating the Eparchy of Bathery. The territory of the Eparchy of Puttur consists of the civil districts of Dakshina Kannada, Chamarajnagar, Chickmanglur, Hassan, Kodagu, Mandya, Mysore, Shimoga and Udupi of Karnataka State.
         On the same day His Beatitude Moran Mor Baselios Cleemis transferred His Excellency Most Rev. Dr.Geevarghese Mar Divannasios from the Eparchy of Bathery and appointed him the first Bishop of the newly erected Eparchy of Puttur. His Beatitude also transferred His Excellency Most Rev. Dr. Joseph Mar Thomas, the then   Apostolic Visitor to North America and Europe and the Auxiliary Bishop of the Major Archieparchy of Trivandrum, and appointed him the third Bishop of Bathery.
Moran Mor Baselios Cleemis Catholicos installed His Excellency Most Rev. Dr. Joseph Mar Thomas as the Bishop of Bathery at St.Thomas Cathedral, on 13 April 2010.
         At present the Eparchy of Bathery compraise of the civil districts of Wayanad, Malapuram, Kozhikode, Kannur, Kasargode of Kerala State and Nilgiris of Tamil Nadu. The ecclessiastical districts of the Eparchy at present are Bathery,Pulpally, Nilgiris, Nilambur, Edakkara, Kozhikode, Mananthavady and Kannur.
         There are 86 priests of the diocesan clergy, three priests from Bethany Ashram and one priest from the OCD congregation who render their dedicated service for the pastoral care of the community. Sisters from Bethany Congregation, Daughters of Mary, Deena Sevana Sabha, Holy Spirit Sisters, FMM Sisters, John the Baptist Sisters are also give their valuable service in the Eparchy.