The first settlement known in the place dates from the Bronze Age (15th century BC). In the 11th century BC it was invaded by the Iapyges, while the Messapic era of the town (as well as for the whole Salento) began in the 8th century BC, to end in the 3rd century BC, with the Roman conquest. Under the Romans, it was of importance for its trade, lying as it did on the sea, at the point where the Via Traiana joined the coast road, 50 kilometers (31 mi) southeast of Barium (Bari). It was famed for its solar and fire cult, which was described by Pliny</ref> and ridiculed by Horace. gave food for laughter and for jest, by its mad wish to make us think that frankincense without the aid of flame will melt upon the threshold of some fane. Let any superstitious Jew think so, but I could not, for I know now from Epicurus that the gods pass their time free from care, and that it is no threatening rage of theirs that sends down from the heavens' lofty dome whatever natural phenomenon we see."</ref></ref>
An episcopal see in the early Christian era, the city was probably abandoned in the High Middle Ages due to the spread of malaria in the area, or to Vandal and Saracen attacks. It remains a titular bishopric of the Roman Catholic church, under the name Egnatia.
The ancient city walls were almost entirely destroyed over a century ago to provide building material. The walls have been described as being 8 yards (7.3 m) thick and 16 courses high. The place is famous for the discoveries made in its tombs. A considerable collection of antiquities from Gnatia is preserved at Fasano, though the best are in the museum at Bari.
- —in Sallentino oppido Gnatia inposito ligno in saxum quoddam ibi sacrum protinus flammam existere—
- "In Egnatia, a town of Salentinum, there is a sacred stone, upon which, when wood is placed, flame immediately bursts forth."<ref name='FOOTNOTEBostock ,<span>,&,</span>, al.1855'>Bostock & al. (1855).
- —Dehinc Gnatia lymphis
Iratis extructa dedit risusque jocosque,
Dum flammâ sine thura liquescere limine Sacro
Persuadere cupit: credat Judaeus apella
- "And then Fasano, built beneath the ban of fountain nymphs,<ref group='n'>"I.e., it had no pure water".<ref name='FOOTNOTEMillington1869[https://books.google.co.jp/books?id=oWQCAAAAQAAJ,<span>,&,</span>,pg=PA41 41]'>Millington (1869), p. 41.
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- Horace (Q. Horatius Flaccus) (1869), A Rhythmical Translation of the First Book of the Satires of Horace, translated from the Latin by R.M. Millington for Longmans, Green, Reader, & Dyer.
- Pliny the Elder (G. Plinius Secundus) (1855), The Natural History of Pliny, London: translated from the Latin by John Bostock & Henry Thomas Riley for H.G. Bohn.