The city occupied a low rocky headland, now called Cape Schisò, formed by an ancient lava flow, immediately to the north of the Acesines (modern Alcantara) stream.

[2] This has become even more definite since 1977 when the marble cippus (or sacred stone) inscribed with a dedication to the goddess Enyo was found in the large sanctuary west of the Santa Venera river.

[citation needed] Hieron, with a view to strengthen his own power, removed the inhabitants of Naxos at the same time with those of Catana, and settled them together at Leontini, while he repeopled the two cities with fresh colonists from other quarters.

[14] The name of Naxos is not specifically mentioned during the revolutions that ensued in Sicily after the death of Hieron; but there seems no doubt that the city was restored to the old Chalcidic citizens at the same time as these were reinstated at Catana, 461 BC;[15] and hence we find, during the ensuing period, the three Chalcidic cities, Naxos, Leontini, and Catana, generally united by the bonds of amity, and maintaining a close alliance, as opposed to Syracuse and the other Doric cities of Sicily[16] Thus, in 427 BC, when the Leontini were hard pressed by their neighbours of Syracuse, their Chalcidic brethren afforded them all the assistance in their power;[17] and when the first Athenian expedition arrived in Sicily under Laches and Charoeades, the Naxians immediately joined their alliance.

With them, as well as with the Rhegians on the opposite side of the straits, it is probable that enmity to their neighbours at Messana was a strong motive in inducing them to join the Athenians; during the hostilities that ensued, the Messanians having on one occasion, in 425 BC, made a sudden attack upon Naxos both by land and sea, the Naxians vigorously repulsed them, and in their turn inflicted heavy loss on the assailants.

An attempt was made in 394 BC by the Rhegians to settle them again at Mylae (modern Milazzo), but without success for they were expelled by the Messanians and from this time appear to have been dispersed in various parts of Sicily.

[25] In 358 BC Andromachus, the father of the historian Timaeus, collected the Naxian exiles together again from all parts of the island and established them at Tauromenium which became the successor of the ancient Naxos.

The site of Naxos itself seems to have been never again inhabited in antiquity; but the altar and shrine of Apollo Archegetes continued to mark the spot where it had stood, and are mentioned in the war between Octavian and Sextus Pompey in Sicily, 36 BC.

[28] Some late Roman construction over the Greek ruins includes a mansio and streets found on the bedrock continuing the general line of the ancient stenopos.