The Archaeological Museum of Pythagoreion is housed in a newly built building in the center of the modern city of Pythagorion, where the ancient city of Samos was located. The exhibition of the archaeological material of the area, chronologically and thematically classified, illuminates aspects of the historical and cultural evolution of ancient Samos from the Neolithic period (4th millennium BC) to the late antiquity (7th century AD).
The collections of the museum include findings from the Neolithic settlement of Kastro and from the geometric necropolis of ancient Samos, pottery from the 9th to the 2nd pre-Christian century, as well as a significant set of sculptures of the Archaic and Roman period.

The most important exhibits of the museum include:

• Marble seated statue of Aiakis, father of the tyrant of Samos Polycrates. It was found in Pythagorion and dates back to 540 BC. According to the surviving inscription, the statue was a tribute to Aryan Hera, from the tenth of the profits he had obtained from piracy.
• Great marble monumental sarcophagus in the form of a monumental building. Second half of the 6th century BC
• A small portico tombstone with a vertigo and an inscription: DIVING THE GIRL. 530 BC
• Marble tombstones with vertigo. Found in Chora. 500/490 BC
• Marble statue of the Roman emperor Trajan, of supernatural size (height 2.71 m)
• Marble busts of the Roman emperors Augustus and Claudius.
• Treasure of 300 Byzantine coins of the 7th c. A.D. From Great Laka.