Ancient writers supply us with only brief information about Gnathia. The city is mentioned by Greek geographer Strabo at the end of the first century B.C., and by the Latin poet Horace, who passed through in 38 B.C. during his famous voyage from Rome to Brindisi (Satire I, 5). These authors, and the later itinerary sources invariably simply mention the position of Gnathia on the sea, on the border between Peucetia (territory of Bari) and Messapia (present-day Salento), at the halfway-point on the major ancient road between Bari and Brindisi.

The earliest human presence in the area dates back to the Late Bronze Age (13th-12th centuries B.C.), with groups of huts scattered along the coast and interland. The most densely settled area was defended by a massive stone wall. This extended around a small peninsula which was destined to became a raised fortified area (the acropolis) as a result of continuous building.

The plant of the city walls dates back to the messapian phase, from the end of the 5th century B.C. These walls, almost 2 km long , protected the city in a semicircle facing inland. Defence walls facing the sea seem only to have been built to the north of the acropolis. The rebuilding and reinforcement of the walls over the centuries is evident from the many different styles of stone-masonry. At the northern corner of the city, the walls are still preserved at their original height of seven metres. Construction of two different phases can be clearly seen, the later reconstruction extending into the pre-existent moat.

Pre-Roman tombs have been found within the city walls, but the true Messapian necropolis are situated outside the city. The changing burial rites of  many centuries have been documented in the western necropolis.

These rich Messapian tombs  were first discovered in the 19th century. “Gnathia pottery” has become a term of international usage; it described pottery made between the middle of the 4th century B.C. and the 3rd century B.C. with decoration in red, white and yellow painted over the black glaze. While archaelogists now know that this pottery was produced in a number of centres in Puglia, the thousands of vases which poured from the tombs of Egnazia from the early 19th century made “Gnathia Pottery” the conventional term.

Around the same time (4th –3rd centuries B.C.) these was a great reorganization of the foot of the acropolis. Here, below a number of more recent buildings, one can recognize a series of  porticoes forming an irregular piazza (agorà), demonstrating the Hellenistic taste of the period.

The region fell to the Romans in the 3rd century (near by Brindisi became a Roman colony in 244 B.C.).The monumental centre of Gnathia bears witness to the “Romanization” of the city. Walking through ancient Gnathia one can view remains of the Civic Basilica, the Shrine of Eastern Divinities, the so-called amphitheatre and the forum. On the other side of the Via Traiana one can find a district of shops, houses and workshops, including a pottery kild and a probable underground storage area for grain, the criptoporticus.

The Via Traiana which runs through the centre of ancient Egnazia, was part of a major new road build by Emperor Trajan in 109 A.D. Starting at Benevento, the Via Traiana gave travellers from Rome to Brindisi a more comfortable alternative to the old Via Appia.

The residential areas of Roman Gnathia have an irregular plan. Houses and workshops are difficult to distinguish from one another, as the structures are usually preserved only to the level of the foundations. Channels and cisterns for the collection of rain-water, and wells to tap the underground water are very common in these Roman buildings.

The Early Imperial period saw the construction of port facilities around the inlet just to the north of the acropolis; the inlet was enlarged and better protected through the construction of two artificial moles.

Between 4th and 6th centuries A.D. the two Early Christian basilicas were built. The larger of the two, with its baptisters, was Episcopal seat of the city. The only Bishop of Gnathia we know of is Rufentius Egnatinus, whore presence is noted at meetings of the Council in Rome in the early 6th century A.D.

The destruction of the city traditionally linked to the invasion of Totila, King of the Goths, in 545 A.D. Egnazia continued to exist at least up to the 9th century A.D., though only as a small groups of people found refuge of Gnathia, converting some Messapian tombs outside the walls into habitations. Life in caves, often with frescoed crypts, was not uncommon between the 10th and 12th century A.D. and other such settlement can be found scattered in the surrounding countryside. Since the 12th century Egnazia has been constantly visited, principally as a source of building material for the nearby centres of Fasano and Monopoli. The 19th century saw a systematic sack of the necropolis, and only in 1912 the official excavations of the city began.