History of the Parish begins before the arrival of the Portuguese Missionaries in India and is one of the Oldest Christian Communities / Parish under the Diocese of Quilon. The Church is situated in Panmana and Chavara Panchayaths of Karunagapally Taluk. As per the Catholic directory the Church was constructed in 1398 and given the name "St. Andrews Church". It was the first church constructed in Karunagapally Taluk as is known as "Karunagapally Pally". Historic records from Udayamperore Sunahadose reveals about the origin of this Church.
Rt. Rev. Bp. Alex Manesious, Bishop of Goa constructed the second Church after Udayamperore Sunahadose which is in Thevalakara and it was known as "Thevalakara Pally". Now this church is under the management of Syrian Orthodox Church and archeologists confirmed records about the construction of the "Thevalakara Pally.
It is worth noting that the present Church has references to three churches. The first church was constructed on the west side of Kottamkulangara temple which is near to Alappuzha and Kollam National Highway. The church was erected in "Kunnickal Purayidom" and there were about 35 catholic families in parish, which spreads towards eastern region to the present Koivila Parish. The said plot "Kunnickal Purayidom" was under Kovilthottam parish property. Due to the movement of the catholic families to the northern side, moreover new conversions taken place, the first church was shifted to "Paniyil Purayidom" it was located two furlong east of the present Church location. Priest home was named as "Kathanar Parsum". As per records land tax has exempted by the Government for the church properties before AD 1070. We can find some of the places and the names "Palliyil & Pathirayam" as the names in the said plots in the records.
The Chavara – Panmana canal passing in front of the present church and was not there before 1749. There were only paddy fields. The said canal was made for irrigation purpose from Panmana Vattakayal to Chavara and land divided into two areas. A book published by Fr. Archilos Mirsmon (1921 to 1942) named "Friars Minors or otherwise Franciscan in India "printed in the Karachi Rotary Press kept in the library of the Tillery Monastery of Franciscans. This book gives valuable evidence about the church in pages 820 & 830 about the parish and the adjoining parishes. In 1749, eight parishes were given to the Franciscan missionaries to look after the parishioners and for their service; Kovilthottam was one amoung the parishes.
During the local war between the rulers, the second church was destroyed by fire and Christian community scattered in and around the panchayaths. Franciscan Provincial of Goa has contributed to the reconstruction of the third Church (Present) because of the two well known Priests of Franciscans served in Kovilthottam church. At that time there were 300 members in the parish. 54 members in Pandharathuruthu Three Kings church (main church of Maruthurkulngara) and 200 members in Karithura Francis Assissi church are also ministered under Kovilthottam church. After the war, the third new church was constructed part by part over a period of time using lime and stone in 1779 by Fr. Yovakim de Santiago.
Fr. Yovakim served the fold and herded the flock diligently with his inborn qualities of humility, concern and care for this parish. Most of the parishioners are under Kodungaloor Diocese. The parishioners are located in the coastal area from Vellanathuruthu to Chavara Light House and on the old church located areas. As per church records six new parishes formed from Kovilthottam parish (Viz.: Vadakkuthala, Karithura, Neendakara, Mamukil, Koivila, Kulangarabhagom).