The neophytes remained normal Christians until the arrival and ministry of St .Francis Xavier in 1542. The Saint had visited Alanthalai a good number of times and wrote two letters on 5/9/1544 to Francis Mansilus camping at Punnaikayal. The place from where he wrote the letters is called SAVERIAR KINARU in Alanthalai. Fr.Henrique Henriques renovated the thatched church in 1558 and named it after St. Peter. Jesuit's report of 1571 vouch this fact.

The population of this hamlet was 800 in 1665 as per remarks of Niogove, the Dutch Captain .The construction work started for St .Antony's church in1698 was completed in 1712 and was consecrated on 24/12/1712 by the Collegiums of Jesuits Rev.Fr.John De Costa. However the building work started for the Church of St. Peter in 1644 was completed only after 1712.

Ministries in Alanthalai were with the Jesuits Priests till 1774. When the Pope Clement XIV decanonised the Society of Jesus, the administration of this Parish changed hands to Goanese Priests till 29.6.1838.The first differences of opinion between the Village Headman and the Church administrators took place only during this period which sowed the seed for future rivalry in the beginning of 20th century. Therefore, the Jesuits again took over after the Society of Jesus reestablished by the Pope Gregory XVI in 1832.It is pertinent to note here that the change over of administration was a smooth affair as far as Alanthalai was concerned according to the letter written by Fr.Martin S.J on 14.7.1838 from Punnaikayal.The first Destitute House was established in 15.1.1854 by Fr.Boshan after obtaining the permission from the Provincial of Madurai Mission Rev.Fr.Verdier.This was later shifted to Adaikalapuram on 16.1.1857 since the inmates were often suffering due to sea breeze. Alanthalai has functioned as a separate Parish since 1693 to 1799.Due to shortage of Priests and the Exodus of seven families to the nearby hamlets Kooduthalai & koottapanai due to internal trouble, the Parish was functioning as a sub station under Virapandian Patnam from 1800 to 1894. During this period the income from the church properties were mostly handled by the Sacristan (Kanakkupillai) and the Village Headman.