Abstract <p>The composition, inner structure, and morphology of zircon grains hosted in various rocks of the Archean Pongoma-Navolok granulite–charnockite–charnoenderbite complex in northern Karelia indicate that these features of the mineral are characteristic and, hence, can be used as indicators of petrogenetic processes that produced the rocks. Zircon was determined to have crystallized from charnoenderbite melt only within the range of high temperatures at which the melt was derived. The charnockitization and granitization of the charnoenderbites were associated with the homogenization of the zircon composition, disruption of its structure, and the dissolution and removal of Zr, Hf, and REE from the charnockitization zone. Growth and dissolution zones in the zircon crystals and zircon grain domains suitable for thermometry and isotope dating were identified, and their relative position in the crystals was determined, using a complex of techniques of high spatial resolution. Temperature evaluations based on Hf distribution between the zircon and melt indicate that the mineral has crystallized in the charnoenderbites only during the earliest evolution of the complex at <i>T</i> = 990–1080°C. When the rocks were affected by charnockitization, some zircon grains reached equilibrium with the autochthonous charnockite melt at the temperature of its generation of <i>T</i> = 790–850°C.</p>