In the centre of Heraklion, steps from Archaeological Museum is the Museum of the defense of Crete. The Museum was founded by the municipality of Heraklion in 1994 and is dedicated to the defense of Crete and national resistance during the Second world war. The aim of the Museum is the collection, preservation and demonstration of historical relics from 1941-1945 properly, as well as documentation and dissemination of information about the people's struggle during the battle of Crete and the German-Italian occupation.

In the Museum exposition presents thousands of original photographs, paintings and drawings of the battle for Crete and national resistance, about 200 books, monographs, essays historical events from 1941 to 1945, hundreds of documents and newspaper articles. The Museum also displays various items related to the war: weapons, uniforms, accessories, household items and much more.

The main part of exhibits covers the "Battle for Crete in may 1941. This battle is one of the largest in the history of the Second world war airborne operation and also known as "Operation mercury". The main purpose of the German invaders was the ousting of the British from the Mediterranean sea and the establishment of strategic control of the Mediterranean basin. The organizer of the militia was a British archaeologist who worked for British intelligence, John Pendlebury. In spite of heavy casualties, the Germans won the battle.

The Museum has its own research center, which focused on the collection of archival materials in wartime different countries (1940-1945) and their translation. The Museum aims to attract the attention of the younger generation to the history of the Cretan people and the awareness of the destructive power of war.