Themistocles, first Archon in the official year 493/2 BC, suspected already that the Persian were preparing an attack and enlarged Piraeus into the biggest port of Athens. In 492 BC the Persian, under the commander Mardonios, advanced on the island of Thassos in Macedonia. The following year they gave an ultimatum to the Greek cities to submit. Some cities did it, while other joined Sparta and Athens to put resistant to the Persian.

The first relevant military campaign between the Persian and the Greeks started in 490 BC. Under the command of the Persian Datis and Artaphenos, a huge army arrived to the island of Eritrea. After six days of siege, the Greek city got finally burnt down and the army set up a base camp there. On the other hand, Callimachos and Miltiades, who were at the front the Athenian army, went into battle in the bay of Marathon, in a small passage that leads to Athens.

The Athenian army, however, was much inferior in number and had to ask for help to the Spartans. But the Persian realized this weak point of their enemies and decided to attack before the arrival of the support. Fortunately, the local circumstances were in the favor of the Athenians, who managed to force back the Persian to their ships. These dropped down the pathetic attempt to attack the Athenian from the west and returned to Minor Asia. So finally Athens won the battle, and they were so proud of it that they recalled it all the time. After this victory, Athens tried to keep its army active and made some attempts to conquer some of the Cyclad islands.

In the political aspect, the years around the the 480 BC were a crucial test to the new Cleisthenic constitution. There were many fights for the political power, many politicians were banned during these years (487 – 482 BC) on the grounds of the ostracism. From 487 BC on, the 9 Archon were not any more elected, but taken out of the 100 nominated Deme, hence decreasing the power of the Areopagus.

A leading person of this time was Themistocles. He enlarged Piraeus into the biggest port of Athens and strengthened the fleet of Athens, known because of its maneuverability and vigorous rowing tactics.