The architectural remains of the Potidaion acropolis are located on the west hillside towards the port and date from the Hellenistic period. They include an inscription, part of the fortification wall, and the remains of retaining walls.

The inscription, which is built into the sea-facing side of the wall that surrounds the modern cemetery, honours the Emperor Trajan, saviour and benefactor of the city of Karpathos and of Potidaion. A little further, on the same side overlooking the sea, is a possible defensive wall of isodomic masonry of the fourth century BC. Terrace walls of polygonal masonry can be seen near the hilltop; the north wall survives to a substantial height, whereas the wall just below the summit is preserved to a great length.

On the slope's most northerly part is an underground cistern for collecting rainwater, with hydraulic mortar on the inside. Other ancient cities of Karpathos have similar cisterns. Another subterranean construction with a rectangular built entrance is visible a little further to the northeast. Ancient walls were also found during the construction of modern houses at the northwest foot of the acropolis, but are no longer visible. The architectural sculptures and stone baptismal font, now on display at the Regional Office square, come from the Early Christian basilica, which was probably located in the same area.