The Greeks of the classical period believed that, in the dark age that followed the collapse of the Mycenaean civilization, significant numbers of Greeks fled and had emigrated to Asia Minor and settled there. These settlers were from three tribal groups: the Aeolians, Dorians and Ionians. The Ionians had settled about the coasts of Lydia and Caria, founding the twelve cities that made up Ionia.

The cities of Ionia remained independent until they were conquered by the Lydians of western Asia Minor. The Persian prince Cyrus led a rebellion against the last Median king Astyages in 553 BCE. While fighting the Lydians, Cyrus had sent messages to the Ionians asking them to revolt against Lydian rule, which the Ionians had refused to do. After Cyrus finished the conquest of Lydia, the Ionian cities now offered to be his subjects under the same terms as they had been subjects of Croesus. Cyrus refused, citing the Ionians' unwillingness to help him previously. The Ionians thus prepared to defend themselves, and Cyrus sent the Median general Harpagus to conquer them.

In the years following their conquest, the Persians found the Ionians difficult to rule. The Persians thus settled for sponsoring a tyrant in each Ionian city, even though this drew them into the Ionians' internal conflicts. On the eve of the Greco-Persian wars, it is probable that the Ionian population had become discontented and was ready for rebellion.