The Church of San Sebastian is located on a hilltop, close to the fish market, in the Northern part of the old town of Lagos. This location offers stunning panoramic views of the Bay. The Church is considered one of the oldest and most beautiful churches in the city.

Even before the Church was built on this place in 1325 there was a chapel of the Immaculate Conception of the blessed virgin Mary. In 1463 Bishop of são joão de Mello contributed to the fact that on this spot a Church was built. In 1490 by order of the king of Portugal, don são joão II, were again carried out reconstruction work, and the Church was expanded. After this the Church was consecrated as the Church of San Sebastian (San Sebastian Church). Unfortunately, as it happened with many historic buildings in Portugal, the Church was almost destroyed in the Lisbon earthquake in 1755. The Church was restored, and two centuries later, the Church was again destroyed by an earthquake, which occurred in 1969. Over time, the Church was again restored.

Inside the Church of three naves that are separated by Doric columns. The original main altar of the Church dates back to the XVI century. The altar consists of four panels. It is assumed that these panels are created by one of the most famous artists of the Algarve in the sixteenth century Alvaro Dias. The Church kept the old plan of the city. In 1828 it was attached to the Church tower with bell.

In 1924 the Church of San Sebastian was entered in the list of monuments of national importance.