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There are three cities of great note. First is İstanbul, straddling the Bosporus, an ancient imperial capital and formerly the center of Orthodox Christianity. Second is the Turkish capital of Ankara, sitting by a Gallatian river of the same name, a tributary of the Sakarya River. Third is the port İzmir on the gulf that shares the city name, south of Lydia.

Turkish and Cypriot Cities

Over a million

Name Metro population (millions)1
İstanbul2 14.4
Ankara3 3.9
İzmir4 2.9
Bursa 1.6
Adana 1.5
Gaziantep5 1.4

Selected smaller cities, or former cities of historical note

Name Alternate names
Antakya Άντιοχεια (Antiocheia), أنطاقيه (Anṭākiyyah), Antioch, Hatay, Θεόπoλις (Theopolis or City of God), Antiochia
Antalya
Bodrum Halikarnnassós, Halicarnassus
Boğazkale بغزكي (Boġazköy, Boğazköy, Boğazköi), Hattuša, Hattusas, Khattushash, Hattusha
Dalaman
Selçuk Ἔφεσoς (Ephesos), Ephesus, Efes, Άγιος Θεόλόγες (Hagiós Theólógos or Holy Word of God), يصلغ (Ayusuluǧ)
Heirápolis
Míλητoς (Milētos) Miletus, ملت6 (Milet)
Πάφος (Pafos) Paphos
Safranbolu
Ἴλιον (Ilion) Τροία (Troia), Īlium, Trōia, Troy
Van Վան, ون, Tushpa, Տօսպ (Tosp),

Footnotes

1. world-gazetteer.com, accessed 3/26/2011.
2. Formerly Kωνσταντινoύπoλις (Kōnstantinoupolis) and قسطنطينيه (Konstantiniyye), both anglicized as Constantinople; Byzantium (Latinized form); and ή Nέα δευτέρα ΄Pώμη (ē Nea, deutera Rōmē; the New, second Rome)--applied to the European portion of the currently bi-continental city.
3. Formerly Angora.
4. Formerly Smyrna.
5. Formerly Ayintap or Antep.
6. I am uncertain about the final (leftmost) consonant. It might have been ط.