The church dates from the early 15th century and was originally dedicated to St John the Baptist, patron and protector of the Knights of St John. The main theme that occupies the church, such us the representation of an Apocalyptic Vision in the conch of the apse, perhaps is associated with the prevailing beliefs in Christendom in this critical period, on the coming of the end of the world.
It was in a ruined state before 1861, when, the Community of Kos decided to undertake its conservation. After the earthquake of 1933, it was found that the church was built upon the important twin sanctuary of Aphrodite. So for the sanctuary to be revealed, it was decided in 1943 to relocate it in a northwest part of the area.
In 1947 the church was dedicated by the Metropolitan of Kos, Emmanuel Karpathiou, to a Koan Neomartyr, St Ioannes Navkleros.