Agios Nikolaos history starts from the mid-Minoan period (2100-1560 BC) however as a city it was settled in the late Bronze Age by the Dorians who established the city of Lato.

Sights:

• The archaeological museum of Agios Nikolaos hosts multiple exhibits from the Neolithic age, Minoan to Roman times.
• The remains of the ancient city of Lato are open to the public.

The  Byzantines liberated the island (395 - 824 AD) until the Saracens Arabs (824 - 961 AD) caped it.

Sights:

• the Panagia Kera Byzantine monastery and the church of Agios Nikolaos.

The Byzantines retook the city in (961 - 1204 AD). After the Crusades (1204 AD) and the end of the Byzantium, Crete was sold to the Venetians. The Venetian hold the city until the whole island was caped by the Ottoman Turks (1648 -1898 AD) who lasted until the proclamation of the Cretan State, later followed by the union with Greece.

Sights:

• the Spinalonga isle with its fort.