The first information about Gnathia dates back to 1561, when Leandro Alberti writes of “i vestigi dell’antica città di Egnazia fra cespugli, urtiche e pruni”, while in the following century there are documents about the first discovery of burials with rich grave goods.

To Francesco M. Pratilli we owe the first schematic plan of the town in 1745 showing the visible monuments of that time, such as the cryptoporticus and the coastal necropolis. The first description of the ancient structures of the town is in the volume entirely dedicated to Egnazia by Ludovico Pepe, written in 1882, where he moreover exposes the common practice of illegal excavations.

With the aim of containing this phenomenon, the official investigations, managed by the Excavations Office with its seat in Taranto, began in 1912 and 1913 and covered a long strip of the old urban structure, where, from north to south, part of the market square, a stretch of the Via Traiana, the residential area south of the road and the southern basilica were brought to light.

Other systematic investigations of the city are from 1963 to 1971. Since 2001, a research programme carried out by the Department of Ancient and Late Antique Studies of the University of Bari “Aldo Moro”, in close collaboration with the Soprintendenza Archeologia of Apulia (Department for the Archaeological Heritage), has been systematically investigating the market square, the district south of the Via Traiana, the episcopal basilica, the area of the acropolis and the district south of the forum with the baths.