Although sporadic finds allow us to hypothesise at least the presence of the site since the Neolithic and Eneolithic periods, there is some evidence of a first settlement on the top of the Ugento hill, corresponding to its southern part, which is now the historical centre, from the Late Bronze Age (12th-10th century BC)

The main necropolis of the archaic and classical era, referable to the Messapian settlement located on the Ugento hill

During the 4th century BC, the construction of the city walls very clearly defined the limits of the city and in this modified urban structure the presence of areas used as necropolis is clear even within the walls, in the areas free of the inhabited area.

Between the 2nd and 1st centuries BC, the topographical organisation of the town gradually changed and if the tombs of the 3rd and 2nd century BC still occupied areas between the different settlement cores, those of the 2nd-1st century BC were mainly located on periphery of the settlement, often in funerary areas already in use in the previous phase

The prehistoric and protohistoric section of the Museum includes a selection of clay and stone materials from Ugento dating back to the Neolithic and Eneolithic period, to which is also added a display case containing ceramic, flint, and bone objects from S. Maria di Leuca.

The numismatic section offers a rich panorama of monetary discoveries in Ugento dating back to the 5th century BC and the Roman imperial period, with some examples even later (from the Byzantine period and the 17th-18th century).

The oldest tombs tracking back to the Messapian settlement of Ugento, and whose grave goods are exhibited in the Museum, date back to the 6th century BC and consist of sarcophagus or coffin burials made of calcarenite slabs, which can also reach considerable dimensions with a so-called semi-chamber structure.

The city walls of Ugento date back to the period of maximum expansion of the Messapian centre, around the middle of the 4th century BC. Their construction took place in a historical moment of great instability and conflict between the Messapian and Tarentini, even if at first the walls mainly responded to the desire of the urban aristocracy to define the urban perimeter and mark the distinction with the surrounding countryside

Among the materials exhibited in the Museum there are some medieval ceramics, mostly fragmentary, that came from the workshops that operated in Ugento, in the Borgo area along the via Salentina, on the eastern slopes of the old town.

The necropolis in the S. Antonio area was excavated in 1986-1987 and consists of about 30 tombs mostly dating from the middle of the4th to the 3rd centuries BC, with the sole exception of the tomb from the archaic period; the necropolis extends just inside the city walls. The grave goods from some of these tombs are on display in the Museum.