In Classical times, the site was uninhabited, but became the site of the Battle of Pylos in 425 BC, during the Peloponnesian War. Pylos is scarcely mentioned thereafter until the 13th century, when it became part of the Frankish Principality of Achaea. Increasingly known by its French name of Port-de-Jonc or its Italian name Navarino, in the 1280s the Franks built the Old Navarino castle on the site. Pylos came under the control of the Republic of Venice from 1417 until 1500, when it was conquered by the Ottoman Empire. The Ottomans used Pylos and its bay as a naval base, and built the New Navarino fortress there. The area remained under Ottoman control, with the exception of a brief period of renewed Venetian rule in 1685–1715 and a Russian occupation in 1770–71, until the outbreak of the Greek War of Independence in 1821. Ibrahim Pasha of Egypt recovered it for the Ottomans in 1825, but the defeat of the Turco-Egyptian fleet in the 1827 Battle of Navarino forced Ibrahim to withdraw from the Peloponnese and confirmed Greek independence.
In the port of Pylos water taxis make the tour of Navarino Bay with stops at the wooden Russian church and the memorials of the French, British and Russian Admirals.