We report two generations of low-δ18O zircons from the Himalayan eclogites and their host gneisses. In situ SIMS δ18O analyses on single zircon crystals (with known age and Hf isotope ratios) from two populations of chemically distinct zircons demonstrate a complex history: (1) an early low-δ18O mantle-derived magma, (2) followed by post-emplacement high-temperature meteoric-water alteration and finally (3) crystallization of new, low-δ18O minerals during the ultrahigh-pressure metamorphism. Magmatic zircon (269Ma) in Group I eclogites yielded δ18O values from 1.9 to 4.6‰ VSMOW with an average value of 4.0±0.2 (n=35, the error is 2SD analytical precision and “n” represents number of analyzed spots), which is lower than the typical mantle values (5.3±0.6, 2SD). In contrast, metamorphic zircons (45Ma) in Group II eclogites preserve unusually low, negative δ18O values from −3.9 to −2.7‰ (average: −3.4±0.4, n=35, 2SD). Zircons in felsic gneiss that surround Group II eclogites have inherited magmatic cores (ca. 260Ma) with δ18O values of ca. 2.9‰, which decrease to −0.1‰ in metamorphic (ca. 45Ma) rims. These zircons preserve lower δ18O values than would be equilibrated with typical mantle. The low-δ18O values in magmatic zircons suggest that the mafic protolith to these eclogites formed from a hydrothermally altered subducted oceanic crust and the negative δ18O values in metamorphic zircons indicate hydrothermal alteration after crystallization of the mafic magmas but before growth of metamorphic zircons. This study reports evidence for melting of subducted low-δ18O ocean crust to form low-δ18O mantle-derived mafic magmas as previously proposed by Cartwright and Valley (1991, Geology 19, 578–581) for Proterozoic Scourie Dikes.