The Catholic Temple of Panaghia was built in the center of Kasteli, among the other official government and private buildings of the city. According to the maps, it seems that between the Temple and Corso there was a residential square. Recent excavations have revealed that this Venetian Temple is built over the foundations of a paleo-Christian Basilica, which was probably a Cathedral Temple of the bishopric of Kydonia during the first Byzantine period. The photographs of the interior and the ground plan that Gerola left us in the beginning of the 20^th century lead to the conclusion that a large part of the paleo-Christian Basilica, and probably the arch of the sanctuary as well, were later incorporated to the new building. According to the references, we can assume that it was a large Basilica with a central aisle, while its side buildings were divided in four chapels.

At its northeast side there was the high bell tower, which was later replaced by a minaret.
The reports of Church officials provide valuable information on the plethora of relics that were kept in the Temple, including many Byzantine icons. In the area around the temple there were other Church buildings, as well as the mansion of the archbishop of Chania. During the Turkish period, the temple was converted into the Mosque of Mousha Pasha to service the large population of Muslims in the area of Kasteli. In the photographs of Gerola we can see the mihrab (a holy alcove for Koran) and the minbar (pulpit) of the Mosque.

After the liberation of Crete, the building was used by the state. During the 1941 bombings, the monument suffered serious damages, and was later demolished because of the new urban plan. Nowadays, the preserved remains of the Temple have been incorporated to private habitations, while its foundations lie under the streets of "Kanevaro" and the plateau of "Aghia Ekaterini".