The Carthaginian settlement was written in their abjad as hmṭwʾ, seems to derive from the Phoenician triliteral root mṭr, which would give it the meaning of "a wool-spinning center". Motya is the latinization of the island's Greek name, variously written Motýa (Μοτύα) or Motýē (Μοτύη). The Greeks claimed the place was named for a woman named Motya whom they connected with the myths around Hercules. The town's Italian name appears as both Mozia and Mothia; its Sicilian name is Mozzia. The island first received the name San Pantaleo in the 11th century CE from Basilian monks.

Motya was famously destroyed by troops from the Greek city-state of Syracuse during the Second Sicilian War in 398 BCE. Not much remained of the city and it was lost to history for centuries, that is until the site was rediscovered in the 18th-century CE on what is now known as San Pantaleo Island.

The excavations brought to light a large number of archaeological finds and many buildings have since been identified.

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Temple of Baal
The temple of Baal (Ba'al)was in use from circa 800 to 396 or 397 BCE. It was one of the most important structures in the enclosed/walled circular area around the sacred pool. The the certain date of its construction is not known, it has been suggested that the earliest construction of a shrine dedicated to Ba'al dates bact to the arrival of the Phoenician settlers on the island. The current remains of the temple structure are oriented approximately east-southeast where the constellation of Orion (known as Ba'al to the Phoenicians)rises at the wintersolstice. A bronze pointer of either a navigational tool or astrolabe was recovered during the excations.

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Sanctuary of Cappiddazzu
The Cappiddazzu sanctuary (Sicilian "cappellaccio", used to indicate a hat with a large brim), is a relatively large sacred area, situated inside the walls, a short distance from the north gate. In a first phase (early 7th century BCE) a series of pits dug into the rock and about 30 cm deep are dated, arranged inside a larger pit, in which bones of sheep and cattle were found, therefore probably used for the sacrifices. In the second phase, attributed to the second half of the 7th century BCE, a first building was built with stone walls, flanked by a well built in the same technique. Architectural fragments of Egyptian groove door capitals relating to a stone building that had to be destroyed in the siege of 397 BCE and whose materials were then reused in the foundations of the reconstructed building are attributable to a third phase of the fifth century BCE. The currently best visible remains refer to the fourth phase, the reconstruction of the fourth century BCE, which consists of a large building with a tripartite plan to the north, inserted in a large enclosure measuring 27.40 x 35.40 meters. In front of the sacred building there is a structure consisting of a rectangular stone slab with a large hole in the center and two semi-holes on the sides, placed within a roughly shaped stone enclosure and probably destined to contain three conical betyls. There are also the remains of a large oval cistern and traces of plaster and floors from different eras (recent essays have identified traces of interventions between the 1st century BCE and the 5th century CE. The remains of a small Byzantine basilica were eliminated in the excavations of the beginning of the twentieth century and are known only from a sketch.

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Barracks
The stucture identified as the barracks (casermette), was most likely a military/paramilitary building. It is located in the southern part of the islan, close to the city wall, which is the only argument for this structure to have been identified as a military building. The structure consisted of several rooms and the presence of remains of a staircase points towards the existence of a second level/floor. Not much is known about the construction date of this structure.

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Sacellum of Astarte
The sacellum or temple of Astarte is located some eighty meters inland inside the southern area of the "Kothon", a natural pond that was later transformed into a sacred pool. It was built some twenty meters north of the Baal temple. The focus of the cult was a rectangular podium/altar joined to the westernwall of the room. The Temple of Astarte was completely rebuilt (circa 500-470 BCE) some three meters to the south of its original position in order to include it within the “Circular Temenos" of Mozia. During this reconstruction it was reoriented to the south, with the entrance looking over the spring of the Temple and the rear side pointing towards the mountain of Eryx, the Elymian-Punic city "upon which Astarte rules".

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House of Mosaics
The House of Mosaics is built on two levels against the city walls on the seashore, suggesting the walls were no longer in use and in ruins. On the upper level is a courtyard with a peristyle paved with a pebble mosaic which is the only example of its type in Sicily. It resembles a panelled carpet with a complex geometric border and with the panels containing depictions of hunting wild animals (a lion attacking a bull, a bird of prey, a deer). Its format dates it from similar ones in mainland Greece and its colonies to the 3rd century BCE. On the lower level in the southwestern part of the house are 6 service rooms with three large pithoi (food storage vessels).

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Tofet
The tophet is one of the most important areas of Motya, an ancient Phoenician sanctuary located near the northern coast of the island. The function of tophets in Phoenician and Carthaginian society is not completely known, but many scholars agree that they were sites where ritualistic sacrifices were performed. The cremated remains of children and urns have been found in the Tophet of Motya. A well, an altar, and a temple also belonged to the complex that was used as a cemetery.