Before the Persian rule that started in the 6th century BC, Miletus was considered among the greatest and wealthiest of Greek cities.

The Archaic Period of Greece began with a sudden and brilliant flash of art and philosophy on the coast of Anatolia.

In the 6th century BC, Miletus was the site of origin of the Greek philosophical (and scientific) tradition, when Thales, followed by Anaximander and Anaximenes (known collectively, to modern scholars, as the Milesian school), began to speculate about the material constitution of the world, and to propose speculative naturalistic (as opposed to traditional, supernatural) explanations for various natural phenomena.

[8] Pollen in core samples from Lake Bafa in the Latmus region inland of Miletus suggests that a lightly grazed climax forest prevailed in the Maeander valley, otherwise untenanted.

Sparse Neolithic settlements were made at springs, numerous and sometimes geothermal in this karst, rift valley topography.

The prehistoric archaeology of the Early and Middle Bronze Age portrays a city heavily influenced by society and events elsewhere in the Aegean, rather than inland.

[8] For some centuries the location received a strong impulse from that civilization, an archaeological fact that tends to support but not necessarily confirm the founding legend—that is, a population influx from Crete.

[citation needed] Homer mentions that during the time of the Trojan War, Miletus was an ally of Troy and was city of the Carians, under Nastes and Amphimachus.

[15] In the last stage of LHIIIB, the citadel of Bronze Age Pylos counted among its female slaves a mi-ra-ti-ja, Mycenaean Greek for "women from Miletus", written in Linear B syllabic script.

Mythographers told that Neleus, a son of Codrus the last King of Athens, had come to Miletus after the "Return of the Heraclids" (so, during the Greek Dark Ages).

This is the mythical commencement of the enduring alliance between Athens and Miletus, which played an important role in the subsequent Persian Wars.

[17] According to Pausanias, the Megarians said that their town owed its origin to Car, the son of Phoroneus, who built the city citadel called 'Caria'.

In the late 7th century BC, the tyrant Thrasybulus preserved the independence of Miletus during a 12-year war fought against the Lydian Empire.

[20] By the 6th century BC, Miletus had earned a maritime empire with many colonies, but brushed up against powerful Lydia at home, and the tyrant Polycrates of its neighbor to the west, Samos.

When Cyrus of Persia defeated Croesus of Lydia in the middle of the 6th century BC, Miletus fell under Persian rule.

[citation needed] In 387 BC, the Peace of Antalcidas gave the Persian Achaemenid Empire under king Artaxerxes II control of the Greek city-states of Ionia, including Miletus.

In this period, the city reached its greatest extent, occupying within its walls an area of approximately 90 hectares (220 acres).

[22] When Alexander died in 323 BC, Miletus came under the control of Ptolemy, governor of Caria, and his satrap of Lydia, Asander, who had become autonomous.

[23] In 312 BC, Macedonian general Antigonus I Monophthalmus sent Docimus and Medeius to free the city and grant autonomy, restoring the democratic patrimonial regime.

In 301 BC, after Antigonus I was killed in the Battle of Ipsus by the coalition of Lysimachus, Cassander, and Seleucus I Nicator, founder of the Seleucid Empire, Miletus maintained good relations with all the successors after Seleucus I Nicator made substantial donations to the sanctuary of Didyma and returned the statue of Apollo that had been stolen by the Persians in 494 BC.

In 295 BC, Antigonus I's son Demetrius Poliorcetes was the eponymous archon (stephanephorus) in the city, which allied with Ptolemy I Soter of Egypt, while Lysimachus assumed power in the region, enforcing a strict policy towards the Greek cities by imposing high taxes, forcing Miletus to resort to lending.

Paul's previous successful three-year ministry in nearby Ephesus resulted in the evangelization of the entire province of Asia (see Acts 19:10, 20; 1 Corinthians 16:9).

The Ilyas Bey Complex from 1403 with its mosque is a Europa Nostra awarded cultural heritage site in Miletus.

There is a Great Harbor Monument where, according to the New Testament account, the apostle Paul stopped on his way back to Jerusalem by boat.

A gradual rise brought a level of about 1.75 meters (5 ft 9 in) below present at about 5500 BP, creating several karst block islands of limestone, the location of the first settlements at Miletus.