The Samothraki mafic suite in the north-eastern Aegean Sea, Greece, is an ‘in situ’ magmatic complex comprising gabbros, sparse dykes and basalt flows and pillows cut by late dolerite dykes. We have determined the age of the complex by SHRIMP zircon geochronology of a gabbro as 159.9 ± 4.5 Ma (i.e. Oxfordian; early Late Jurassic), which precludes any correlation with the so-called Lesvos ophiolite further south (253.1 ± 5.6 Ma; Latest Permian). Six distinct, hitherto unrecognised, geochemical groups have been identified among the basalts and dolerites of the Samothraki mafic suite on the basis of trace-element and Nd–Sr isotopic characteristics. All groups show the presence of an enriched component in their source region, be that a long-term enriched mantle reservoir or an enriched melt. They also invariably show evidence of the addition of subduction-related hydrous fluids. Some groups testify to recent depletion events of long-term enriched mantle, some to the involvement of strongly depleted, recently refertilised mantle, and others to significant addition of melts either from subducted sediments or continental crust. None of the groups bear resemblance to mid-ocean ridge or back-arc basin basalts thus suggesting that the Samothraki mafic suite cannot represent mature back-arc basin crust. In view of recent advances in back-arc basin geology and the data collected here, the Samothraki mafic suite could represent a slab-edge segment of an evolved back-arc basin near the trench, a situation that satisfies the inflow of fertile mantle, the strong signature of sediment melts and the rare occurrence of boninite-like melts. Alternatively, it could represent the embryonic stages of back-arc basin formation either by a propagating rift tip into continental crust or by oblique subduction causing back-arc rifting of continental crust and creation of nascent transtensional basins. Restoration of block configuration in NE Greece before extensional collapse of the Hellenic hinterland and exhumation of the Rhodope Metamorphic Core Complex (mid-Eocene to mid-Miocene) results in a continuous ophiolite belt from Guevgueli to Samothraki, thus assigning the latter to the Innermost Hellenic Ophiolite Belt. We propose that the Samothraki mafic suite originated via rift propagation of the Sithonia ophiolite spreading ridge into the Chortiatis calc-alkaline arc (and its basement) which was partly assimilated. Our model does not favour southward intra-oceanic subduction of the Meliata–Maliac Ocean under the Vardar Ocean whereby Samothraki is located in the back-arc spreading centre. The autochthonous rift-related origin, the enriched geochemical characteristics and the lack of common features with known ophiolite types suggests calling the igneous complex of Samothraki Island a “mafic suite” rather than an “ophiolite”.