The ancient island of Ikos which is later (16th century) referred to as Liadromia or Chiliodromia and from 1831, as Alonissos, is the only inhabited island in the National Marine Park.

The history of the region, as of all the islands of Northern Sporades, is important. The oldest findings are from the Stone Age, when the islands joined to the Pelio Peninsula. Tools are petrified bones from the Middle Stone Age have been found at Kokkinokastro on Alonissos. These are possibly the oldest findings indicating human settlement in the Aegean. Signs of a New Stone Age settlement have been discovered in the bay of Saint Peter on the island of Kyra Panagia.

The first known inhabitants were the Dolopes, a tribe related to the Pelasgi. References have been found to offerings to the oracle at Delphi from residents of the wider area during the classical years. In 478BC the island belonged to the Athenian Alliance. In 403BC they were conquered by the Spartans, but were regained by the Athenians a few years later. During the wars between the Macedonians and the Athenians, the islands came under the influence of Phillip of Macedonia and became prosperus. In 146BC they were conquered by the Romans.

In the 3rd AD century, the inhabitants embraced Christianity. As part of the Byzantine Empire, the islands flourished economically and culturally, as witnessed by monuments of the time (churches, monasteries and fortifications). The unhabited islands surrounding Alonissos were important monastic centers and many of these still belong today to the monastery of Megesti Lavra of Mount Athos.

After the capture of Constantinople by the Crusaders, the islands became the property of Western feudal lords. After the Ottomans broke up the Byzantine Empire in 1453, the area was taken over by the Venetians. It was devastated in 1538 by the raids of the Turkish fleet under the command of the pirate Barbarossa. In the 16th century, the island was reinhabited by a greek population under ottoman occupation. The inhabitants took part in the prerevolution uprisings against the Turks and in the revolution of 1821. The Treaty of London (1830) included the Northern Sporades and the present area of the Park in the newly established Hellenic State.