The site was founded in the Bronze Age as Ithome, an ancient city originally of Achaean Greeks which eventually came under the hegemony of the military state of Sparta with which it had a long struggle.

Late Roman Messene suffered much after the major AD 365 Crete earthquake that hit hard also the entire SW Peloponnese.

It will be in the so called Byzantine "Dark-Ages" during the 7th and 8th centuries that the city once again experienced a deep crisis with the settlement of new populations in the region, probably of Slavic origin.

Excavation of the site began on April 10, 1829, with the French scientific commission of the Morea Expedition, under the direction of Guillaume-Abel Blouet, at the end of the Greek War of Independence.

Epaminondas resolved to support an independent Peloponnesus by building three fortified cities, Megalopolis and Mantinea in Arcadia and Messene in Messenia.

In 85 days the combined armies and exiles guided by the engineers and artisans had completed the walled city of Messene over the site of the previous Ithome.

"[14] As the Arcadians are known to have spoken a dialect closely related to Mycenaean Greek, the exiles restored were not from the original Achaean refugees of the return of the Heracleidae, but were the Doricised population that developed in the 7th century BC under the subsequently dispossessed Heraclid dynasty of Messene.

The wall was pierced by two main gates flanked by protective structures and rectangular in shape with a lintel of a single, massive beam of limestone.

Pausanias has left a description of the city,[15] its chief temples and statues, its springs, its market-place and gymnasium, the Asclepieion,[16] its place of sacrifice, the tomb of the hero Aristomenes and the temple of Zeus Ithomatas on the summit of the acropolis with a statue by the famous Argive sculptor Ageladas, originally made for the Messenian helots who had settled at Naupactus at the close of the third Messenian War.

[3] The other buildings which can be identified are the theatre, the stadium, the council chamber or Bouleuterion, and the propylaeum of the market, while on the shoulder of the mountain are the foundations of a small temple, probably that of Artemis Laphria.

[3] As Messene continued to be an important urban center of SW Peloponnese all through Late Antiquity, a considerable number of Early Christian and Byzantine monuments have been excavated and are now visible and partially restored.

From the sixth century dates a large three-aisled basilica built near the old Theater of the city, at an area where a Christian cemetery had developed.