Ayia Napa is mentioned for the first time by Leontios Mahaeras (a Cypriot choreographer) in 1366 A.D. and a second time by the same in 1373 in his account of the shipwreck of five Venetian ships loaded with booty, which the Venetians had stolen during the looting of Cyprus. The next mention of Ayia Napa is encountered in Venetian documents and maps of the 16th century. Due to the lack of sufficient historical evidence, this study is based mostly on archaeological findings and the local tradition.

The area around the monastery of Ayia Napa was not inhabited until 1790 when (according to local tradition) there arrived from Thessaloniki a group of people who left their homeland fleeing an outbreak of cholera (the plaque). Finally, only two of them survived the deadly disease, a man by the name of Nicholaos Kemitzis and his son. Later the son married a Cypriot girl from a small village called Panayia which was found on the hills north of the monastery where the water of Ayia Napa comes from. The young couple did not settle in Panayia because of a bitter conflict between the inhabitants of Panayia and Turkish authorities of Famagusta concerning the supply of water. Instead, they sought to establish a safer home outside the monastery thus beginning the village which was to also be named "Ayia Napa" after the shrine.

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