Relict blocks of massive metabasalt occur within foliated epidote amphibolites that are interlayered in the Paleozoic metapelitic-metapsammitic sequences of the Southalpine basement near Bressanone, Eastern Alps. The original magmatic clinopyroxene–plagioclase–opaque association in metabasalt is variably overprinted by a static alteration, which encompasses a wide spectrum of mineral assemblages. A high-temperature alteration stage is recorded by topotactic overgrowth of Fe-Ti-rich clinopyroxene on primary Fe-poor clinopyroxene, precipitation of datolite and Fe–Ti–rich clinopyroxene (±calcite, chlorite and Co–Ni sulphides) in amygdales, and formation of albite-enriched patches in plagioclase. In places, the primary pyroxenes are partially replaced by kaersutite ± Ti-biotite. In the most altered metabasalts, a probably lower-temperature alteration assemblage, made of Fe-rich and Ti-poor clinopyroxene, calcite, titanian garnet and datolite, replaces the cores of the magmatic pyroxenes. Late veinlets of Fe-rich and Ti-poor clinopyroxene (with minor datolite, garnet and sulphides) are accompanied by further alteration of magmatic clinopyroxenes into chlorite + smectite ± talc, further albitisation of plagioclase, filling of amygdales by datolite ± calcite ± chlorite ± Ca-rich garnet, and precipitation of disseminated sulphides. The alteration sequence recorded in the metabasalts predates the Variscan regional metamorphism recorded by the host amphibolites and is interpreted as being related to circulation of hydrothermal fluids in a submarine continental basin with active magmatism. The lithostratigraphic and structural analogies between the Paleozoic basements of the Southalpine (e.g. Gudon) and Austroalpine (Northern Greywacke Zone) domains of the Eastern Alps, as well as the presence of hydrothermally altered mafic layers in both, suggest that magmatism and associated submarine hydrothermalism in these two domains were related to similar extensional processes affecting the pre-Variscan continental crust, which were possibly synchronous (middle Paleozoic) at the regional scale.