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The prehistoric temple in ix-Xewkija, first recorded by Gann-Frangisk Abela, points to some activity in the area and it is possible that the place was inhabited since very early times. Trial excavations carried out in 1904 by the archaeologist Father Manwel Magri in the fields east of the parish church confirmed that the area was inhabited since Neolithic times. Around 700 BC, Malta and Gozo were colonized by the Phoenicians and later by their descendents, the Carthaginians. Several Punic objects were discovered in the limits of Ix-Xewkija at Tal-Morob. The Romans took over in 218 BC at the beginning of the second Punic War, creating Gozo a municipium independent of Malta. The Romans turned the Citadel into their acropolis and a town developed beneath its walls. The Xewkija area was definitely inhabited in Roman times. The place was probably dominated by a rustic-type Roman villa, a villa intended for agricultural industrial activity, especially oil-pressing.

In 535 AD, these islands passed under the dominion of the Byzantines, until in 870 AD, when Aghlabid Arabs attacked Malta and left the archipelago depopulated. Around 1045, a group of Saracens came over from Sicily and recolonized the island. The toponym Ix-Xewkija must have originated soon afterwards. In 1091, Count Roger the Norman established suzerainty over Malta, which later passed into the hands of the Swabians (1194), the Angevins (1266), and the Aragonese (1282). During this time the islands were governed by a series of feudal lords. Their rule was mitigated from around 1350, when Gozo and Malta were incorporated on and off in the royal domain. A local government known as the Universitas Gaudisii was formed to defend local interests.