The boundary between the Helvetic and the Penninic (=Briançonnais) Zones has long been recognized as a major fault (“Penninic Front”) in the Western Alps. A narrow oceanic domain has been postulated at least along part of this boundary (the Valaisan Basin). However, the information provided by the pre‐Triassic basement has not been fully exploited and will be discussed here in detail. The igneous and metamorphic history of the pre‐Triassic basement shows significant differences between the External Massifs from the Helvetic Zone, with abundant Late Carboniferous granites, and the basement of the Briançonnais Zone, including the Internal Massifs (Dora‐Maira, Gran Paradiso, and Monte Rosa), devoid of Carboniferous granites. A major coal‐bearing basin, the “Zone Houillère,” opened along this boundary. This limnic intramontane basin has never been properly investigated. The Zone Houillère is not comparable with the external, paralic, flexural, basins on both sides of the Variscan belt but shows similarities with the Saar‐Saale Basin. Like the latter, we interpret the Zone Houillère as a transtensional basin opened along a major, crustal‐scale, fault zone, namely, the East Variscan Shear Zone. The Permian magmatism and sedimentation displays contrasting distributions, being absent or very localized in the Helvetic Zone, and widespread in the Penninic Zone. The above data indicate that the structural inheritance from the Variscan belt plays a major role in defining the future location of the Valaisan Basin, that is, the boundary between the European paleomargin and the Briançonnais microcontinent.