We present results of zircon LA-ICP-MS U–Pb, Lu–Hf, and trace-element study in combination with whole-rock Sm-Nd and Rb-Sr isotope data on the magmatic rocks of the Markov Deep and Ashadze hydrothermal field (Mid-Atlantic Ridge). Zircon from three gabbronorite samples in the Markov Deep defined an U–Pb ages between 0.90 ± 0.02 and 2.00 ± 0.05 Ma, with the youngest age found in the deepest sample. Zircons from four samples of gabbros and trondhjemites of the Ashadze Field have identical ages: from 1.04 ± 0.07 to 1.12 ± 0.09 Ma. Plagioclase troctolite from the Markov Deep (sample I-1069/19) contains exotic zircon grains with ages widely ranging from 90 Ma to 3.2 Ga, which is inconsistent with age of the rocks in the Mid-Atlantic Ridge. Several hypotheses are discussed to explain the origin of such exotic grains, in particular, their formation at mantle depths, or reaching these depths with subducted crust, and others. Experimental study of zirconium solubility shows that the mafic and ultramafic melts could be oversaturated with respect to zirconium only at unrealistically high contents, which usually do not occur in the corresponding rocks. Entrapped xenogenic zircon must be dissolved in the mafic and ultramafic melts and its finds in these rocks presumably indicate its disequilibrium precipitation. Zircon could be formed in the intrusive mafic rocks at the final stages of fractional crystallization, which explains the presence of own zircon in gabbroids. Zircon is very stable in crustal magmatic processes, especially at lowered activity of alkalis, but almost instantly (on geological scale) loses radiogenic lead by diffusion way under upper mantle conditions (1300–1500°C). While applying REE distribution for interpreting zircon origin, as many as possible elements should be analyzed to discriminate between intrinsic zircon element distribution and anomalies caused by defects in its structure.