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The church of Agios Nikolaos is located at the small cove where ships were stranded during the Byzantine and Venetian eras. This is an exceptionally old domed church, one of the few of the Early Byzantine era that survive on Crete, with an impressive apse over the altar. It was built before the Arab conquest, thus the original murals of the 8th-9th century, i.e. the Iconomachy era, are aniconic. In the 14th century, the church was renovated and many murals were covered by new ones.

The church is of great value, being one of the few examples of Early Byzantine architecture on Crete, as its original form did not undergo significant changes. The city of Agios Nikolaos is named after this church.