St Xavier Church was worked by St Francis Xavier in the 1600s, in Kanyakumari. St Francis Xavier was a minister from Goa, who frequented Kottar. He was known by the name 'Valiya Pandaram' among the masses.According to history, St Francis Xavier turned away the Padagas from attacking Travancore. The ruler allowed him a plot at Kottar, which had housed a congregation before. St Francis Xavier constructed the congregation on the site contiguous the Church of St. Mary.
St Xavier Church was later redesigned in 1865 and the Church of St. Mary was assumed control. In the year 1930, St Xavier Church rose to the status of a Cathedral.In 1942, a pinnacle to respect St Francis Xavier was built. A cave for St. Mary and a minor hallowed place for St. Ignatius were likewise developed inside the premises of this house of God.