—We present results of a study of the morphology, internal structure, and chemical composition of oceanic zircon, which show that zircon is a sensitive indicator of tectonic and physicochemical processes occurring in the lower oceanic crust. Crystallization of magmatic zircon in gabbroids is not an instantaneous process; it proceeds in the course of differentiation of parental melts in the tectonically active mid-ocean ridge (MOR) setting. The main geochemical indicator of crystallization differentiation during magma cooling is an increase in Hf content toward the zircon grain edge. Zoning is also observed in magmatic zircons from oceanic plagiogranites (OPG), but it is weaker, apparently because of the narrower temperature range of zircon crystallization in these rocks. The OPG zircons are depleted in REE as compared with the least altered magmatic zircons of gabbro, which is probably due to the formation of OPG during the partial melting of gabbro with the participation of concentrated water–salt fluid, a derivate of seawater, and due to the co-crystallization of zircon and apatite. High-temperature hydrothermal processes within slow-spreading MORs lead to a partial or complete recrystallization of zircon as a result of dissolution/redeposition. A significantly reduced cerium anomaly and the presence of microinclusions of xenotime, uranium and thorium oxides or silicates, and, sometimes, baddeleyite in zircon alteration zones indicate a reducing type and high alkalinity of the hydrothermal fluid. The fluid, a derivate of seawater, acquires these features during circulation near the axial zone of ridges as a result of phase separation in the system H2O–NaCl and interaction of the fluid with abyssal peridotites of oceanic core complexes. The estimated solubility of zircon in basic melts indicates that even near-solidus crystallization of zircon is highly unlikely in anhydrous basaltic melts but is possible in differentiates of deep-seated hydrous basic magmas. The Ti-in-Zrn geothermometer must be used with caution, because variations in the Ti content in zircon might be controlled not only by temperature but also by other factors, especially when mineral inclusions in zircon testify to a drastic change in its growth (dissolution) conditions. A geothermometer based on the distribution of Zr and Hf between zircon and the host rock has several advantages over indicators of the crystallization temperature of magmatic zircon that are based on the zircon saturation index and the content of Ti in zircon. It does not depend on the composition of melt and on the correct estimates of the SiO2 and TiO2 activity. In addition, reconstruction of the Zr and Hf fractionation trends during crystallization of zircon from granitoid melts makes it possible to evaluate the temperature of separation of more differentiated melt fractions.