The underwater archaeological research in Pythagorion provided with the evidence to categorize it as 'enclosed' military harbor.

The 'enclosed' military harbor became the symbol of an ancient city's not just naval but military as a whole power, as it's the core of her military endeavors.

The well fortressed military harbors are the heart of the city's defence.

The ancient Samos, a key- city for northeastern Aegean, developed on her own an important harbor, whose topography is as following:

On the north side, the wall-jetty starts from the point that the land fortification meets the coastal wall and continues 170 m to the south, right then continues to the west forming a right angle around 85 m length. At the meeting point of the land fortification and the coastal wall, seems that there was no tower.

On the other hand, along the coastal wall two square towers are indicated. This coastal wall (διατείχισμα) isolates the military harbour from the ancient city, no entrance gates have been traced.

On the outside of the walls-jetties two ripraps of great size develop. The riprap at north, meets the wall-jetty and therefore it also reaches around 170m length.

South, at the point of a tower and with direction to the east, the renown choma of Polycrates «χώμα του Πολυκράτη» starts, which apparently continues indepedently further south than the wall-jetty, towards east and 480m length.

The site plan of the ancient harbour is as following: the walls-jetties to the North and South define the space of the ancient harbour letting a narrow opening , for the entrance and exit of the ships.

So that two ships can sail in this narrow opening, meaning the one entering and the other exiting, it should have been at least 20m maximum, taking into account that the military ships were about 6m wide. This opening is placed to the east , in the same direction as the modern harbour entrance.

This 'enclosed' military harbour constitute one of the first examples of this kind that evolved in Greece and seemingly was built in 530 B.C., during Polycrates tyranny, and remained constantly in use till now.