During the period from the 12th to the 15th century when parts of Greece were under the control of Venice, Pylos became known by the Italian name Navarino. In 1827 the bay of Pylos was the site of the Battle of Navarino during the Greek War of Independence.
Bronze Age Pylos was excavated by Carl Blegen in 1952. It is located at modern Ano Englianos, about 9km north-east of the bay. Blegen called the remains of a large Mycenean palace found there the "Palace of Nestor," after the character Nestor, who ruled over "Sandy Pylos" in the Homeric poems. Linear B tablets found by Blegen clearly demonstrate that the site itself was called Pylos by its Mycenean inhabitants. This site was abandoned sometime after the 8th century BC and was apparently unknown in the classical period.
The site of classical Pylos was probably on the rocky promontory now known as Koryphasion at the northern edge of the bay of Pylos. This site is described by the Greek historian Thucydides in his History of the Peloponnesian War. In 425 BC the Athenian politician Cleon sent an expedition to Pylos, to seize and occupy the bay. The Athenians captured a number of Spartan troops on the adjacent island of Sphacteria (modern Sfagia, see Battle of Sphacteria). Spartan anxiety over the return of the prisoners, who were taken to Athens as hostages, contributed to their acceptance of the Peace of Nicias in 421 BC.