The island's archaeological importance is highlighted through museums and archaeological collections. The Archaeological Museum of Heraklion houses the most important findings of the Minoan civilization. Treasures dating back from the Neolithic to the Roman Era can also be viewed in the archaeological museum of Chania, Rethymnon, Sitia, Kissamos, Ierapetra and Archanes. The new museums of Messara and Ancient Eleftherna are in operation, while the museum of Agios Nikolaos is under maintenance. Important local archaeological Collections operate at in Myrtos and Gazi.
The collection of the Minoan antiquities in the Archaeological Museum of Heraklion is the largest in the world and the museum is considered the main Museum of Minoan civilization. It is classified as one of the largest and most remarkable museums in Greece and one of the most important in Europe.
The Museum of Ancient Eleftherna is the first museum inside and archaeological site in Crete, as it is located next to the ancient city of Eleftherna. The three halls of the museum host the whole history of Eleftherna from 3000 BC city to 1300 AD with everyday objects and artworks.
The Archaeological Museum of Chania is located next to the Venetian harbor and is housed in the church of the old Venetian monastery of Agios Fragiskos (St Francis) of the Franciscans. The exhibition is divided into two major sections. The eastern section hosts findings from the Neolithic until the Late Minoan period.
The Archaeological Museum of Rethymnon is temporarily hosted in the basilica of Agios Fragiskos (St Francis) in the old town of Rethymnon. It hosts exhibits from various excavations around the prefecture of Rethymnon which represent all periods from the Neolithic Age to the Roman period.
The Archaeological Museum of Sitia operates since 1984 and hosts the most important archaeological finds from eastern Crete (from Sitia, Palekastro, the islets of Mochlos and Psira, the necropolis of St. George, the palace of Zakros, the Hellenistic town of Xerokambos, Ziros, Makrigialos, Lefki island and ancient Itanos).
The Archaeological Collection of Malevizi exhibits about 500 ancient objects, dating all from the seasons of Cretan antiquity. The majority of the exhibits come from the collection of Metaxas, which was maintained by Nikolaos Metaxas from 1959 to 1997.
The Archaeological Museum of Agios Nikolaos was founded in 1970 and houses findings from the Neolithic Age, the Minoan Era and the Graeco-Roman Times from the Lassithi prefecture.