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7 museums selected in this guide.

The Nikos Kazantzakis Museum is a small but moving museum dedicated to Crete's most famous writer, author of Zorba the Greek and The Last Temptation of Christ. Located in the village of Myrtia (Varvari), 20 km south of Heraklion, it occupies the renovated family home and showcases the author's personal effects, manuscripts, and letters.
The Museum of Christian Art (also called the Collection of Saint Catherine) is housed in the 15th-century Church of Saint Catherine of Sinai, adjacent to the Cathedral of Saint Minas. Its collection of Byzantine and post-Byzantine icons, frescoes, and liturgical objects is among the finest on Crete.

The Heraklion Archaeological Museum is one of the most important museums in Europe and the finest repository of Minoan art and artifacts in the world. Completely renovated and reopened in 2014, its 27 galleries span from the Neolithic era to the Roman period. It is the essential companion to a visit to Knossos.

CretAquarium Thalassocosmos is one of the largest aquariums in the Mediterranean, located at the former US military base in Gournes, 15 km east of Heraklion. Operated by the Hellenic Centre for Marine Research, it showcases over 2,500 marine organisms from 250 species native to the Mediterranean and tropical seas.

The Historical Museum of Crete covers the island's story from early Christian times (4th century CE) through the Byzantine, Venetian, Ottoman, and modern eras. Housed in a neoclassical mansion on the waterfront, its collection complements the Archaeological Museum by continuing the chronological narrative where Minoan civilization ends.
The Natural History Museum of Crete, run by the University of Crete, explores the geological and ecological history of the eastern Mediterranean through interactive exhibits, dioramas, and a large earthquake simulator. It is the largest natural history museum in the eastern Mediterranean region.

The Lychnostatis Open Air Museum, located in Hersonissos 26 km east of Heraklion, is a lovingly curated ethnographic museum showcasing traditional Cretan life, crafts, and agriculture. Spread across garden terraces on a hillside, it features reconstructed workshops, a chapel, a windmill, and herb gardens.