Before the arrival of the Phoenicians, the outer coastal area of the Sinis Peninsula, as well as much of the rest of the area, was a zone of extensive Nuragic presence, a prehistoric or protohistoric civilization that was named after the nuraghi.
The main Nuragic complex in Tharros area is certainly the village erected on the highest point of the hill of Su Murru Mannu, the same area later occupied by the Phoenician tophet. It is a large settlement with circular huts built using the basalt rock widely available in the area and arranged around a common space. It was assumed that a single tower-like nuraghe rose on the highest sector of the site, but this has never been determined with certainty. The materials recovered during the excavations conducted by V. Santoni help to date these structures from the final stages of the Middle Bronze Age and also indicate that the settlement was probably abandoned at the time of the arrival of the Phoenicians. The discovery of artifacts at different sites in the Tharros area however, suggests the survival of a Nuragic settlement even in the early stages of the Iron Age.

Two other nuraghi are located on Capo S. Marco. One of them, Nuraghe Baboe Cabitza (many of the nuraghi have been named), is located in the central and highest part of the promontory and was used as the basis of a lookout post during the Second World War. The other one, located in the cove of Sa Naedda at the southeastern side of the Capo S. Marco, is now almost completely destroyed. A Nuragic monument was also assumed to be located at the base of the Spanish tower on the hill of St. John.