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Although much is known about the Ordovician tectonics of the South European Variscides, aspects of their geodynamic evolution and palaeogeographic reconstruction remain uncertain. In Sardinia, Variscan tectonic units include significant vestiges of Ordovician evolution, such as a fold system that affected only the Cambrian–Lower Ordovician successions, and are cut by a regional angular unconformity. A comparison of the stratigraphy and tectonic structures of the successions below and above the Lower Ordovician unconformity and a reinterpretation of biostratigraphic data allow us to identify significant differences between the stacked tectonic units. The unconformity is sealed as follows: (i) in the Sulcis–Iglesiente Unit (Variscan External Zone, SW Sardinia) by Middle–Upper Ordovician continental and tidal deposits; and (ii) in the Sarrabus and Gerrei units (part of the Variscan Nappe Zone, SE Sardinia) by Middle–Upper Ordovician calc–alkaline volcanic rocks. Therefore, at the same time, one tectonic unit was situated close to a rifting setting and the others were involved in a convergent margin. Of note are the different durations associated with the unconformities in the tectonic units (17 Myr in the Sulcis–Iglesiente Unit, 6 Myr in the Sarrabus and Gerrei units) and the occurrence (or absence) of glacio-marine deposits indicating that the units were located at different palaeo-latitudes during the Ordovician. These results suggest that the SW and SE Sardinia blocks did not share the same geodynamic setting during the Ordovician, implying that they were situated in different palaeogeographic positions at this time and subsequently amalgamated during the Variscan Orogeny. Furthermore, stratigraphic and tectonic correlations with neighbouring areas, such as the eastern Pyrenees, imply alternative palaeogeographic reconstructions to those proposed previously for some peri-Mediterranean Variscan terranes.