The seat of the municipality was the town of Pythagoreio, formerly known as Tigani. The town was renamed in 1955 to honour the locally born mathematician and philosopher Pythagoras. The port of the town is considered to be the oldest man-made port of the Mediterranean Sea.
Pythagoreio is built on the ancient city of Samos. Some ruins of the ancient city are today incorporated in modern houses of Pythagoreio. The ancient city reached affluence around 530 B.C. under Polycratestyrant. At that time Samos became a powerful nautical state. This power led to richness and prosperity, which is evident from great works of the period, such as the great aqueduct (part of it is the Tunnel of Eupalinos), temple of Heraion, and Samos harbour. Today many of these works can be seen in the modern town and nearby area. The ancient fortification also remains.
Samos was conquered by Persians and declined for a while. Samos flourished again for two short periods: First during the 3rd century under Ptolemy's rule (when lived Aristarchus), and second under Roman rule. The ruins of Roman period are visible today, about half a kilometre west of Pythagoreio. The harbour of Samos remained important during Byzantine period. Ruins of the Byzantine period are visible in the area of Logothetis' Tower on the west side of the harbour.
Samos totally declined during Frangokratia, when the coastal settlements depopulated. In the later Ottoman period the centre of the island was Chora, built inland, 4 Km northwest of Pythagoreion. During Greek War of Independence the Samian Leader Lykourgos Logothetis built a tower in Pythagorion between 1824 and 1827. In 1831 Logothetis built a church near the tower. Between 1859 and 1866 the new harbour was built in the same place as the ancient harbour, after which the settlement started to develop. The name of new settlement was originally Tigani, but in 1955 renamed to Pythagoreio after the name of famous ancient Greek Mathematician and Philosopher from Samos Pythagoras.
Pythagoreio is one of the most toured places of Samos since it has many archaeological sites as well as a big sandy beach. The most important sights in Pythagoreio and the nearby area are:
Tunnel of Eupalinos: It’s about the most famous sight of Samos. The Tunnel of Eupalinos, 1036 meters long, was part of an ancient aqueduct. It is located about 2 Km northwest of Pythagoreion.
Heraion of Samos: a very important archaeological site, with sanctuaries dedicated to Hera. It is located about 4 Km west of Pythagoreio and, along with Pythagoreio, has been designated a World Heritage Site by UNESCO.
Harbour of ancient Samos: The ancient harbour is located in the same place as the new harbour. Some ruins are visible today. The ancient harbour is referred to by Herodotus, who described it as a great work of Polycrates' period for mostly martial use.
Ancient theatre: a theatre of Roman period. It has been renovated and it is used for the local cultural festivals.