Sparse eclogite exposure in accretionary-to-collisional orogens cannot only reveal the sites of ancient subduction zones and plate boundaries, but also elucidate the multi-stage tectonic evolution in the Wilson cycle. The southern part of the Dora-Maira Massif in the Western Alps is well known for its ultrahigh-pressure (UHP) rocks and contains small occurrences of petrographically distinct types of eclogite. Due to the lack of detailed geochronological and geochemical data on these rocks, the nature of their protolith and related geodynamic setting has remained unknown. In the current study, 33 samples from 13 localities were studied by whole-rock major- and trace-element analysis, and a selection of the samples were studied using Sr-Nd-Hf isotopes, as well as high-resolution elemental mapping and U-Pb geochronology of zircon. According to macroscopic appearance, petrography, chemical composition, and principal-component analysis of multi-elements, two major types are distinguished. Light-colored eclogite is phengite-rich, commonly foliated, bears kyanite and quartz/coesite, shows relatively high MgO, K2O, SiO2, εNd(t) (−2.2 to +1.4), and εHf(t) (+3.5 to +7), with a protolith geochemically similar to an enriched-type mid-oceanic-ridge basalt (E-MORB). Dark eclogite generally is massive, rutile-rich, shows higher values of Ti, Fe, P, Nb, and Zr, εNd(t) values between −2.8 and −0.8, εHf(t) values between −6.1 and −3.2, with an oceanic island basalt (OIB)-type protolith composition. Magmatic zircon cores, which are characterized by steep heavy rare earth element (HREE) patterns and negative Eu anomalies, yield consistent protolith ages of ca. 253−252 Ma in both eclogite types. Metamorphic zircon domains with flat HREE patterns and insignificant Eu anomalies yield a younger mean age of ca. 34 Ma, which is the age commonly assigned to eclogite-facies UHP metamorphism. Considering the various geochemical signatures of E-MORB- to OIB-like eclogites and the regional tectonic evolution, their protolith is best explained as rocks, which crystallized from rift-related basaltic magma, associated with the break-up of the Pangea Supercontinent that eventually resulted in the birth of the Piemonte-Liguria Ocean (Alpine Tethys Ocean) between the future Eurasia and Adria plates. Therefore, the UHP eclogites in the Dora-Maira Massif likely fingerprint a multi-stage tectonic evolution from divergent (continental extension, rifting) to convergent (subduction zone) plate boundary, corresponding to the beginning and end of a Wilson cycle. Incidentally, they reveal that mafic rocks in the Alpine basement units may not be polymetamorphic, but may actually consist of post-Variscan products that underwent only Alpine metamorphism.