Lithological comparisons between building stones of an archaic sanctuary on Despotiko (Cyclades) and geological units mapped on this island enabled a distinction to be made between locally derived and possibly imported material. The most common lithologies used in the main sanctuary building (Building A) were medium-grained white calcite marble with thin, rose-coloured dolomite marble layers (Marble 1), coarse grained, white calcite marble (Marble 2), white mylonitic gneiss and grey granitic gneiss; dark grey banded calcite marble and yellowish calcarenite were rarely used. Excepting Marble 2, all building stones in Building A occur on Despotiko and could originate from the island. The occurrence of nine quarries (presently undated) in the surroundings of the sanctuary, seven in white mylonitic gneiss, one in dark grey calcite marble and one in a white calcite marble resembling Marble 1, support a local provenance. Submerged archaeological structures within Despotiko Bay, a classical marble inscription from the sanctuary and partly submerged agriculture trenches at the east coast of Despotiko all suggest that the relative sea-level there was > 3 m lower in the Early Bronze Age and > 1 m lower during Hellenistic times. If vertical tectonic movements are neglected, the present sea-floor bathymetry indicates that an isthmus linked Despotiko, Kimitiri and Antiparos until at least Hellenistic times.