The history of Alonissos is lost in the depths of the Paleolithic era where the first traces of inhabitancy are found. The present Alonissos took its name during the first years of Greek liberation and it has no relation to the ancient Alonissos. During the antiquity, the island was named Ikos, and Alonissos was the name that was used by the ancient Greeks, probably for the neighboring island, north of Kyra Panagia.
The legend says that during the 16th century BC, Cretans with their leader, the mythical Stafylos who introduced winemaking to the island, settled in Ikos and Skopelos. The Minoan settlement soon adopts a Mycenaean character and moves in the location of Kokkinokastro, east of the island.
During the Classical period, the inhabitants of Alonissos were worshiping the god Poseidon. In the 3rd century AC, the inhabitants accepted Christianity as their religion. In 190 BC, the island is occupied by the Roman fleet but there is little information on the years that follow up to the occupation of Constantinople from the Franks in 1204 AC, assuming that Alonissos and its neighboring islands came under the Frankish rule. Along with Skopelos, Alonissos met several conquerors throughout the centuries.
After the occupation of Constantinople from the Turks in 1453, the islands were under Venetian rule and remained that way until 1538, when the Turkish fleet, ordered the Turkish authority. During the Greek Revolution of 1821, many Greeks from different places of Greece arrived in Alonissos. Together with the locals, they form the present population of Alonissos.
An important point in the recent history of Alonissos is the severe earthquake of 1965. This earthquake damaged most houses in Chora and made the inhabitants move to Patitiri, the port of Alonissos.