Although the first references on the monastery of the Augustinian order, one of the most important monasteries of the Venetians in Rethymno, dates to the 2nd half of the 16th century, it is almost certain that its foundation goes back in earlier years.
According to certain Venetian maps and the excavation reports the monastery had a rectangular plan with the cells arranged around the church. Today only the church is preserved with its original plan altered because of its conversion to a mosque and the addition of a chapel at the west. The initial church was a single-naved Basilica with large windows and a saddleback roof. The principal entrance was at the north side and it is one of the most important Venetian portals of the town. Its design is based on a drawing of the 16th century Italian architect Sebastiano Serlio. On the west is still preserved the small chapel of Corpus Cristi built in 1617.
After the Fall of Rethymno by the Ottomans, Gazi Deli Huseyin Pasha, the commander-in-chief of the ottoman army in Crete and the conqueror of Rethymno, founded in the area a complex which included a mosque, a poor-house, a library and a school. Huseyin Pasha used the church to a mosque, the chapel to a library and the nearby monastery of the Franciscan order to an imaret (poor-house). On the west of the mosque was built in 1980-1891 a minaret with two balconies. Its total height is 33m.
The monument was restored in 1986 and is now used as a conservatoire, a concert hall and a lecture hall.