The construction of the castle was begun in 1402 on the site of the former Seljuk fortress by the Knights of the Order of St. John of Jerusalem, who arrived from the Greek islands of Rhodes and occupied the castle through the  difficult times of Bodrum. They occupied it until 1523 when it was captured by Süleyman the Magnificent, who overpowered the knights in 1523 and kept the castle for the next  400 years. 

The chapel was then converted to a mosque by Süleyman the Magnificent and a minaret was added.  After remaining empty following the First World War; in the early 1960s it became the home of the Bodrum Museum of Underwater Archaeology 

The construction of the fortress was carried out under the leadership of the German knight  architect Heinrich Schlegenholt and much of  the marble columns and stones came from  the Tomb of Mausolus, the ruler of Caria (377–353 BCE). The tomb is one of the seven wonders of the ancient world.

The castle is one of the best examples of fortification devices of its time and included everything necessary to prevent attacks both from the sea and from the land: several observation towers, seven  gates and a tunnel. The fortress-castle was always ready for defence and was reliably guarded. The inner territory of the castle was divided by language into a zone guarded by one or another group of knights. There  are the English, German, French, Italian and Spanish towers, which have their own characteristics and history.

The castle also houses the Liman Tower or Port Tower, which today serves as the main entrance to the castle. There is a secret tunnel built for emergency evacuation, connecting the castle with the ancient amphitheatre of Bodrum.