The city's name comes from the word κολοφών, "summit", (which is also the origin of the bibliographic term "colophon", in the metaphorical sense of a 'crowning touch',) as it was sited along a ridgeline.

Colophon was the strongest of the Ionian cities and renowned both for its cavalry and for the inhabitants' luxurious lifestyle, until Gyges of Lydia conquered it in the 7th century BC.

After the death of Alexander the Great, Perdiccas expelled the Athenian settlers on Samos to Colophon, including the family of Epicurus, who joined them there after completing his military service.

Notium served as the port, and in the neighbourhood was the village of Clarus, with its famous temple and oracle of Apollo Clarius, where Calchas vied with Mopsus in divinatory science.

In Roman times, after Lysimachus' conquest, Colophon failed to recover (unlike Lebedos) and lost its importance; actually, the name was transferred to the site of the port village of Notium, and the latter name disappeared between the Peloponnesian War and the time of Cicero (late 5th century BC to 1st century BC).

[5][6][7] Colophon continued to be listed in Notitiae Episcopatuum as late as the 12th or 13th century, as a suffragan of Ephesus, capital of the Roman province of Asia.