Two years after the destruction, on September 1573, the Rector Alvise Lando laid the foundation stone of the castle, which was to be built according to the drafts of Sforza Palavicini. After a large number of modifications, the fortress was finally completed in 1590. The general draft of the fortress provided new forms of defence, which had become necessary, since gunpowder had come into use: The polygonal ground plan included bastions whilst the walls were wider and inclined.

In reality however, due to the morphology of the land only three bastions could be built to the South and to the East, while the north wall formed three peaks. In general the draft of the fortification wall was not the best possible, since it limited defensive abilities. The rocky surface, which impeded an appropriate construction, the lack of a moat, the limited free space around the fortress resulting from the inhabitants' refusal to demolish their houses were some of the basic factors, which limited successful defensive action.

Contrary to that the infrastructure of the interior space was probably well planned: Public buildings were situated at a distance from the wall, the ammunition storerooms were housed at the safe north side, and a square formed the centre of the fortress.

The interior of the fortress accommodated the following basic buildings: the storeroom of the artillery, where canons and weapons were kept, the residence of the Councillors, where one of the city's two Venetian councillors lived, the residence of the Rector, which represented a luxurious, magnificent building in the central square of the fortress.

West of the central square and opposite the cathedral the Rector's residential premises were built, part of which have been preserved up to today. The building was founded in 1575 and completed in 1582, and it was first occupied by the Rector Anzolo Barocci.

He continued to modify the building up until 1584, because he considered it to be too high and exposed on the hill of Aghios Athanassios, in the west of the city. The imposing and luxurious style of the building is testified to in written records of that time referring to 49 doors, 81 windows, two staircases as well as galleries.

Unfortunately, none of the buildings of this complex could be preserved, except for part of the prison, which Barocci had built east of the main residence, and for the cathedral, which was situated opposite the remarkable residential complex of buildings and was dedicated to Aghios Nikolaos.

The temple of Sultan Ibrahim was built on the ruins of the cathedral of San Nicolo during the Turkish occupation. New elements such as the large semi-circular dome, the apse of Michrab in the centre of the southeastern side as well as the minaret, which was built next to the entrance, characterised the transformation of the cathedral into a Muslim temple.

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The fortress of Monopari
After the 4th Crusade Crete was turned over to Bonifatius of Montferrat, who at a later date sold the island to the Venetians.

However, in 1206 the Genovese pirate Enrico Pescatore conquered and besieged the island, and only as late as 1210 did the Venetians succeed in recapturing it. One of the fortresses built by Pescatore is the Fortress of Monopari (Bonripario), remnants of which can be seen from the top of the precipitous hill of Kastellos near the village Ano Valsamonero. Being already a natural stronghold the site merely demanded the construction of a wall at the north side of the hill, which provided the only access.

Although the fort has not been restored, one can clearly distinguish two rows of walls at the north side, including three towers for the protection of the entrance, as well as the remains of buildings, two of which were probably storerooms, a cistern and a well.