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The town of Samos is the capital of the island. The town is built amphitheatrically, on a hillside sloping down to the shore that forms the curve of a long U-shaped bay. It is one of the few towns that managed to retain its traditional character, boasting a beautiful waterfront and many neoclassical buildings bearing witness to its prosperous past. Its former name was Limin Vatheos or Kato Vathi and served as a harbour for the village of Vathi. The town took the name Samos in 1958.

The town's centre comprises the port and the square, built in 1864 based on a design by French engineer Bouchet, who also supervised its construction. In 1882 the square was named Pythagoras. The town's other sights of interest include the numerous neoclassical public buildings, which give the town its unique character; the Governor's palace, built in 1875 halfway along the waterfront promenade; the Hospital building, the Pythagorean Gymnasium, built in 1882, now housing the town's 1^st Primary School, the Prison, which today houses the Samos Prefecture branch of the General State Archives.

Worth seeing are also the buildings of the Elementary School (1897), the imposing building of General Assembly, which housed the conventions of the General Assembly members from 1901, and later accommodated the Mayor's offices, the Municipal marketplace, the Courts of Justice (1901-1909), the Customs building, the Mavrogeneios Vocational School (1902) in Malagari and the Paschalio Archives Centre and Museum (1909-1911). Church-wise, the town is divided into four parishes: Saint Nicholas, Saint Spyridon, Saint Theodoros and Saint Charalambous.