According to a myth, the creation of the Cyclades and specifically Heraklia is attributed to the god Poseidon. It is said that the sea god transformed the Cycladic nymphs into islands to punish them because their behavior had angered him.
Although the historical and archaeological data we have about Heraklia are few, they can help form an image of the island's history.
During the Proto-Cycladic period (3rd millennium BC), the existence of two small settlements on the island, at the sites of Kampos Agios Athanasios and Agios Mamas, whose inhabitants were engaged in agriculture, animal husbandry and fishing, have been established. In Agios Mama, the cemetery of the settlement with box-shaped graves, where clay vessels and marble figurines were found, has also been identified. An obsidian blade from Milos was also found at the cape of Agios Georgios, in the NE. From this we conclude the small participation of the island in the commercial activities of the Proto-Cycladic period when we had the development of sea trade routes and the flourishing of navigation.
In historical times, and especially during the Hellenistic period (4th-2nd century BC), the fortified site of Kastro, near Livadi, belongs to it. The fort has impressive high square towers and inside it traces of habitation can be seen during many and successive periods of historical times (Hellenistic, Roman). Inside the fort was the Temple of Zeus and the Sanctuary of the goddess Tyche (Tycheo). The continuous habitation of Heraklia during historical times is proven by the scattered archaeological finds in many parts of the island.
During modern times and specifically during the Ottoman period, evidence suggests that the closed and inaccessible coves of the island were ideal hideouts for pirates who roamed the Aegean. The activity of the pirates at that time largely determined the daily life and habits of the inhabitants of the small island. Towards the end of the 18th century and until 1826, the largest part of the island turned into barren lands and few fields were arable ("shares") for the needs of the monks of the monastery of Hozoviotissa of Amorgos or even lands for grazing their flocks , because Heraklia belonged to the property of the monastery.
In the year 1826, the illegal settlement of some residents of Aegiali Amorgos began, who began to clear the island. In 1831, however, the Monastery allows other Aegialites to come to Heraklia and signs a ten-year contract with them with the right to own and exploit the land and share the products by 50%. We do not have more information about the island's recent history. After the revolution of 1821, it joined the newly established Greek state, like the rest of the Cyclades islands. In 1941, in the context of the occupation of the Greek territories by the Axis Powers, Heraklia was initially under Italian administration, while after the capitulation of Italy, in 1943, the island experienced German occupation until its liberation, in 1944.