The Chuktukon alkaline carbonatite complex is a part of the Chadobets complex, situated in the southwestern part of the Siberian craton. It is composed principally of aillikite-damtjernite and carbonatite and a host of Nb and REE mineralisation. Zircons were collected from drillhole samples of the damtjernites and hydrothermally overprinted carbonatites. Zircon grains show oscillatory zoning and a significant signature of recrystallization in cathodoluminescence images. Oscillatory zoned zircons preserved primary signatures, whereas recrystallization processes were related to infiltration of carbonatite melt and late stage fluid. The recrystallization led to different changes in the zircon geochemistry and appearance of multiphase inclusions with mineral composition, which is common of carbonatites (alkali-rich carbonates, fluorcalciopyrochlore, fluorapatite, Ba-Sr-RЕЕ-Ca-carbonates, calcite, dolomite, phlogopite and others). Hf-isotope composition of oscillatory zoned and recrystallized zircons is similar and records the signature of their primary heterogeneous source, with ɛHf(t) varying from 6.3 to −0.6. U-Pb age of oscillatory zoned zircon from damtjernite shows that the rock was emplaced at 256.7 ± 1.1 Ma, indicating that the Chuktukon intrusion was coeval with the Permian-Triassic Siberian Traps (252–250 Ma) and extensive alkaline magmatism in the Siberian craton.