The Santa Marija Tower on Comino formed part of the early system of towers which the Order set up to facilitate defence and communication between the Ċittadella in Gozo and Mdina. It later became a key location of the system of towers built along the coast. The decision to build this Tower was taken by Grand Master Alof de Wignacourt in 1618, and was financed by the Grand Master himself, by the sale of the brushwood on the island and from the profits made by the resettled farmers. The site chosen was some eighty metres above sea level.
The design of the Tower was square in plan with four corner turrets. The bulk of the Tower is twelve metres high and stands on a plinth some eight metres high. A three metre wide strip was laid along the top surface of the plinth to enable the defenders to move easily to any endangered point. The walls of the Tower are about six metres thick and the four corner turrets are extended perpendicularly and crowned with a battlement top.