The capital and port of Nissyros is Mandraki, built in the northwest of the island among the foothills. Its white houses stand out in great contrast with the dark volcanic terrain. Quite a few traditional houses retain the natural shading of the stone.
1.5 km east of the capital is Loutra renowned for its spa springs which are still in operation today.

East of Loutra lies Palli, a quaint fishing village.
Southeast of Mandraki set in the island's interior is Emborios. It is built amid an area rich in olive trees, fruiting trees, figs and grapevines and has a hot steam spring with therapeutic properties.

Nikia stands at an altitude of 400 m with a view to the sea. Its white houses, coloured door and window frames and tiled roofs blends in perfectly with the vegetation in the area.