This paper synthesizes available and original U-Pb geochronological and hafnium and oxygen isotope data on zircon from gabbro and peridotites in the oceanic core complexes (OCC) of the Mid-Atlantic Ridge (MAR) extending for 2000 miles along its crest zone. We attempted to reproduce the evolution of MAR magmatism and to determine the geochemical and geodynamic nature of zircon protolith in OCC. We show that the relicts of old continental lithosphere have been preserved locally beneath the axial ridge zone and were involved in the partial melting of a shallow mantle during the entire magmatic evolution of the MAR rift valley. Age variations of zircon from plutonic rocks of the oceanic basement of fracture zones at some distance from the rift valley suggest young magmatism that differs in age from established magnetic anomalies. During the geological history of the Atlantic Ocean, the evolution of the melt originated in the rift valley of MAR, with zircon crystallization at the final stages, was influenced by aqueous (or aqueous–saline) fluid. Obtained conclusions confirm the fundamental significance of the interaction between hydrothermal and magmatic systems in the slow-spreading mid-ocean ridges.