The petrogenesis of the world famous Koktokay No. 3 pegmatite in the Chinese Altai Mountains is still enigmatic due to its superenrichment of rare metals and the apparent absence of a parental granite. We present results from a granite apophysis that was recently discovered in the No. 3 pegmatite open pit. Results show that it has low K/Rb (32.35−38.76), Zr/Hf (13.78−23.30), Nb/Ta (1.00−6.02), and extremely low K2O/Na2O (0.12−0.20) ratios, which, together with its mica composition and the occurrences of garnet, indicate that it is a highly evolved muscovite albite granite. Columbite and apatite from the granite apophysis yielded U-Pb ages of 182.3 ± 1.0 Ma and 184.9 ± 4.3 Ma, respectively, which are younger than the Triassic ages (ca. 210 Ma) of the main magmatic stage but fall into the age range of the No. 3 pegmatite series (220−175 Ma). Both the granite and the apatite grains within it share nearly identical rare earth element patterns with the magmatic stage of the No. 3 pegmatite. The whole-rock εHf(t) values (t = 183 Ma) range from −0.11 to +1.32, consistent with those of the No. 3 pegmatite and indicating a similar source. We propose that the Jurassic granite represents a late pulse of magma injected as apophyses from a deep-seated magma chamber (perhaps from the lower crust), which overlapped with the early pegmatite and promoted the rare metal mineralization. The No. 3 pegmatite and the Jurassic granite may represent a continuous magmatic system with a 50 m.y. melting process, generating this unusual giant pegmatite intrusion with abundant rare metals.

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