Precise measurements of submerged archaeological markers in the Siracusa coast (Southeastern Sicily, Italy) provide new data on relative sea-level change during the late Holocene. Four submerged archaeological sites have been studied and investigated through direct observations. Two of them are Greek archaic in age (2.5–2.7 ka) and are now 0.98–1.48 m below sea level; the other two developed during the Bronze age (3.2–3.8 ka) and are now 1.03–1.97 m below sea level. These archaeological data have been integrated with information derived from a submerged speleothem collected in a cave located along the Siracusa coast at − 20 m depth. The positions of the archaeological markers have been measured with respect to present sea level, corrected for tide and pressure at the time of surveys. These data were compared with predicted sea-level rise curves for the Holocene using a glacio-hydro-isostatic model. The comparison with the curve for the southeastern Sicily coast yields a tectonic component of relative sea-level change related to regional uplift. Uplift rates between 0.3 and 0.8 mm/yr have been estimated.