Aghios Nikolaos was built on the site of the harbour town for Lato, an important city-state of yore. An old harbour town, it was known as Lato pros Kamares.
The two shared a floruit in the Archaic and Classical eras, had their own currency and worshipped the Goddess Eileithyia, the patroness of childbirth, Lato pros Kamares hit its peak about 800-700 BC, dominating and controlling the surrounding countryside. This city-port continued to exist after its mother-city had vanished, down to the 6th c AD, but from then on until the 13th century there is precious little information available.
After the distribution of the Byzantine Empire at the hands of the Crusaders, Crete was sold to the Venetians. However, prior to their taking control of the island, Genoese pirates ravaged the island: in 1206 the Genoese Enrico Pescatore had built on the hill Kefali an imposing castle which he named Mirabello because of the Beautiful View it commanded over the neighbourhood. From the castle, both the bay and the administrative district took their name – Mirabello or Merambello.
A little later on the castle and area were reclaimed by the Venetians. With the passing of the centuries, and after sundry disasters - natural and otherwise, the castle was finally destroyed in the 17th c AD by the Ottoman Turks.
In the time of the Venetian presence, the port continued to witness important trading activity, though the settlement was chiefly occupied by fishermen.
With the imposition of Turkish rule in 1645, the settlement was gradually abandoned. If one speedily moves to the final years of Turkish rule, the old village was reinhabited, taking the name of Mandraki. This gradually metamorphoses into the town of Aghios Nikolaos. This, its full and present name, comes from a small Byzantine church of the 7th c AD, sited on a small peninsular across from the seaside road.
At the start of the 20th c AD, the capital of the Lassithi Prefecture was moved here – a few decades later saw the advent of the tourist boom.