Settlement in the city area dates back to the pre-Minoan period. Architectural remains have been found from the end of the Neolithic period to the Bronze Age.

The city flourished during the Classical, Hellenistic, Roman and Byzantine periods as one of the island's most important ports. During Venetian times, the city was destroyed three times: first by an earthquake in 1508, then by Turkish pirates in 1538, and finally by the Venetians themselves in 1651. This last destruction occurred during the Cretan War. Lacking the resources to withstand a prolonged siege by the Turks, the Venetians destroyed the fortifications and relocated the garrison to Heraklion. The inhabitants migrated west, and the town remained deserted for the next 200 years of Turkish rule. The city was rebuilt after the Cretan Revolt until 1870. Today it has almost 20,000 inhabitants.

The Archaeological Museum features finds from the wider area, dating back to the period between 3500 BC and 500 AD.
Some of the pithoi are adorned. This one has a row of griffons.