It is believed that Pythagorio is built on the remains of Ancient Samos. Very close to the village you will see the famous Efpalinio Trench, the ancient aqueduct that dates back to the 6th century.

Irodotos called it "amfistomon trench". It was built by mechanic Efpalinos. It is a 1040m tunnel stretching from the north side of mountain Kastro to the south. In 2 to 9 m depth is the canal with the pipe that transferred water to the town. According to historic sources this aqueduct was used during the ancient and roman times.

At the same area, 8 km from Pythagorio is Ireo. The most important archaeological site in the island, the temple of Hera. It was a grandiose monument and one of the most important devotional temples of its time.