Phocaea was an ancient city located at the northern entrance to the bay of Smyrna, near the estuary of the Hermos River. It was a city in the province of Asia. It is listed in many episcopal notitias as suffragan of Ephesus and later (from the 10th century onward) of Smyrna. Constantine VII Porphyrogennetos, however, omitted Phocaea from his list of the poleis of the theme of Thrakesion. Byzantine historians mention Phocaea as a geographical site, without any social or economic characterization.

Theodore Karantenos won a naval victory over the fleet of Bardas Skleros in 977 near Phocaea.  Around 1088, Tzachas conquered Phocaea and made it the base of his maritime operations. It was a commercial port, and Alexios I included Phocaea in the list of coastal towns in which the Venetians were granted privileges. The importance of Phocaea rapidly increased from the end of the 13th century after it was ceded by Michael VIII to the Genoese family of Zaccaria and became the center of alum production and trade. Probably sometime between 1286 and 1296 the stronghold of New Phocaea was erected to the north of the old town, which came to be called Ancient (Palaia) Phocaea.

The two cities suffered from a naval assault of the Catalan Grand Company in 1307 or 1308. Among the precious objects carried away as loot were, according to local tradition, a piece of the Holy Cross, the shirt made by the Virgin for St. John the Apostle, and the manuscript of the Apocalypse written by St. John himself. Although Andronikos III managed to conquer New Phocaea temporarily (probably in 1336) with the help of his Turkish allies, the cities remained in the hands of the Genoese throughout the Palaiologan period. The Gattilusio family seized control of Ancient Phocaea around 1402, and a Greek inscription of Dorino I Paleologo Gattilusio, "authentes of Palaia Phocaea," dated in 1423/4, was found there. In 1455 both towns fell to the Ottomans.