Some 3,000 years ago, the low-lying area was a lagoon linked to the Ionian Sea.  This strategic position at the end of today’s Ksamili peninsula led to the city’s foundation. The foundation legend of the city involved Helenus son of King Priam who attempted to sacrifice a bull on his ship which escaped and leaped ashore before dying. On the same spot, the city was founded. Virgil, the Roman court poet of the Augustan age, immortalized Butrint by making it one of the places where his hero, Aeneas, paused on his long voyage to Italy.

The earliest settlement at Butrint was probably restricted to the acropolis hill, which belongs to the Late Bronze Age on the eastern slope. The city eventually became the focal point of a local tribe, the Praesaebes, themselves part of a larger grouping the Chaonians that were one of the tribes of the region known as Epirus, a mainland state with relations to both Illyrians to the north and Greeks to the south.