The history of Agios Nikolaos begins in ancient times when it was the port for Lato, a powerful city during Hellenistic times. The harbour was still used during Roman times and the first Byzantine period although its importance had diminished. After this, it disappeared from history only to reappear in 1206 when the Genoans built the fortress of Mirabelo and gave its name to the town and bay. An earthquake destroyed the fortress and no trace of it remains. In the 16th century, the Venetians gave the town its current name, taken from the chapel of Agios Nikolaos on the peninsula of Limena. During the Turks' rule the town was uninhabited and only after 1870 did people move here, mainly to escape from Turkish persecution.