Agios Nikolaos was settled in the late Bronze Age by Dorian occupants of Lato under the name Lato pros Kamara, often simply Kamara. It was the port of Lato for a long time. In the 2nd century BC, Lato was abandoned, and many citizens settled in Kamara. The name of the present-day town comes from the church of Agios Nikolaos, which dates back to the 9th or 10th century and is one of the oldest intact churches in Crete.

In 1970, the Archaeological Museum was opened to house finds from Eastern Crete that had previously been housed in Heraklion

This object is known as the "Goddess of Myrtos"

It is a rhyton (drinking vessel) found near Myrtos on an altar inside a home shrine. It's a depiction of a female figure holding a beak spouted pitcher, which serves as the only opening of the rhyton. It is believed to have been used for ritual libations. This vessel is from the Early Minoan period (around 2500-2300 BC)