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The rising Kingdom of Lydia, ruled by the famed King Croesus, conquered these Greek city-states. The city-states were able to secure a great deal of autonomy and continued to flourish, under the Lydians. This arrangement was upset by the rise of the Persian Empire, based in modern Iran, which is often regarded as the first ‘World-Empire.’ <ref>Holland, p 3</ref> Cyrus the Second, sometimes known as the Great, conquered the Median and Neo-Babylonian Empires and annexed the kingdom of Lydia, thereby establishing the Achaemenid Empire, the first Persian Empire.
The Greek cities in Ionia were also annexed by Cyrus. The Achaemenid monarch and his successors respected local customs and religions and gave regions in their realms’ considerable autonomy.<ref> Fine, JVA The Ancient Greeks: A Critical History (Harvard, Harvard University Press, 1983) </ref>. However, the Ionian Greeks who were very urbanized and their democratic political systems proved very difficult to fit into this system. To control the Greek cities, Cyrus appointed his son, Darius also adopted local rulers with dictatorial powers, who were answerable to a Persian satrap or governor and this policy. This caused great unrest in cities such as Ephesus and Colophon, which had traditionally been democracies’, but this was ignored by the local Persian Satrap.<ref> Hornblower, Simon The Greek World: 479–323 BC (4 ed.) (Abingdon: Routledge, 2011),p. 2 </ref>
In 500 BC the Satrap of Asia Minor held an assembly with the rulers who governed the Ionian cities in the name of Darius. There was increasingly rivalry among the tyrants, as they were known, and each sought to expand their territories at the expense of their neighbors. To preserve peace and stability in Ionia, the rulers were obliged to ally and foreswore to attack each other. However, in BC 499, Aristagoras, the tyrant of Miletus sought to conquer the independent island of Naxos and add it to his territories. He tried to win support from his fellow Ionian tyrants’, but they refused. Aristagoras then secured some powerful Persians support and sought to conquer Naxos in the name of Darius.<ref>Herodotus, v, 118</ref>