The existing castle was built by the Venetians in 1579. Its original name was Stinαlonde, but was later renamed Spinalonga from the Venetian island whichis today called Giudecca. Due to its strategic importance, the Spinalonga castle was occupied by the Venetians for 50 years after the fall of Handakas. Spinalonga was then occupied by Turkey in 1715.

At the end of last century it was a municipality of its own with Turkish residents until 1903, when Crete decided to isolate those suffering from lepracy and create the hospital on Spinalonga, in order to facilitate those afflicted by the Hansen disease.

The difficulties of those who remained on the island until 1957 has marked and emotionally charged the island establishing it a place of suffering and rememberance.