The Venetian 'occupation' of Crete began in 1252, when the town of Kydonia was captured by the Venetian Navy, and lasted for 393 years, through until the town fell to the Ottoman Turks in August 1645. During this period, the island itself was renamed Canea. The Venetians constructed the inner (docklands) harbour and outer (trading) harbour and mole we see today, between c.1320 and c.1356, with the lighthouse being constructed between c.1575 and c.1600.

The current lighthouse was rebuilt during the period La Canea was occupied by Egyptian troops (1824 - 1832), and consequently is styled in the form of a minaret. The tower is divided into three sections, with three different plan shapes. The lower section is octagonal, the middle section has sixteen sides, and the upper section is circular.

The lighthouse underwent extensive restoration in 2005/2006, and is now fully restored and operational.