In situ U–Pb dating and trace element analysis of zircons, combined with a textural relationship investigation in thin section, is a powerful tool to constrain the ultra high-pressure stage of high-grade metamorphism. Two types of zircon grains have been identified in thin sections of a retrograde eclogite from the main hole of the Chinese Continental Scientific Drill project in the Sulu UHP terrane. Type 1 zircon grains occur as inclusions in fresh garnet and omphacite, and Type 2 zircon grains were found in symplectite around omphacite. The fresh rims of Type 1 zircons and mantles of a few Type 2 zircons exhibit remarkably lower REE, Y, Nb and Ta contents than the inherited zircon cores, suggesting coeval growth with garnet, rutile and apatite during UHP metamorphism. These may have formed in the UHP metamorphism and survived retrograde metamorphism. The weighted average 206Pb/ 238U age of these zircon domains (230 ± 4 Ma, 2 σ) agrees well with the published age of coesite-bearing zircon separates (230 ± 1 Ma, 2 σ), suggesting that the peak UHP metamorphism in the Sulu terrane may have occurred at ~ 230 Ma. Zircon domains surrounded or cut across by symplectite could have been altered by retrograde metamorphism. Together, they provide a younger weighted average 206Pb/ 238U age of 209 ± 4 Ma (2 σ). These retrograde zircon domains have similar REE compositions to the ~ 230 Ma UHP zircon domains. These observations imply that the ~ 209 Ma zircon domains could have formed by fluid activity-associated alterations in the amphibolite-facies metamorphism, which could have resulted in the complete loss of Pb but not REEs in these domains.