On the eastern beach of the Spinalonga peninsula, in the bay of Kolokytha, there is another basilica, which, according to the surface indications, is directly connected with an inhabited area, as well as with the operation of the port there.

The temple has at least two building phases. The original one dates back to the 5th century, while the second one to the time of the emperor Justinian, around the middle of the 6th century A.D., when the original wooden roof of the basilica was replaced by vaults and a central dome. In the second phase, the temple was decorated with rich sculptural decoration from marble of Prokonisos, which was manufactured in the workshops of Constantinople.

Based on the testimony of the coins, the use of the basilica is documented until the 7th century A.D.