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The microstructures, major- and trace-element compositions of minerals and electron backscattered diffraction (EBSD) maps of high- and low-Cr# [spinel Cr# = Cr 3+ /(Cr 3+  + Al 3+ )] chromitites and dunites from the Zedang ophiolite in the Yarlung Zangbo Suture (South Tibet) have been used to reveal their genesis and the related geodynamic processes in the Neo-Tethyan Ocean. The high-Cr# (0.77–0.80) chromitites (with or without diopside exsolution) have chromite compositions consistent with initial crystallization by interaction between boninitic magmas, harzburgite and reaction-produced magmas in a shallow, mature mantle wedge. Some high-Cr# chromitites show crystal-plastic deformation and grain growth on previous chromite relics that have exsolved needles of diopside. These features are similar to those of the Luobusa high-Cr# chromitites, possibly recycled from the deep upper mantle in a mature subduction system. In contrast, mineralogical, chemical and EBSD features of the Zedang low-Cr# (0.49–0.67) chromitites and dunites and the silicate inclusions in chromite indicate that they formed by rapid interaction between forearc basaltic magmas (MORB-like but with rare subduction input) and the Zedang harzburgites in a dynamically extended, incipient forearc lithosphere. The evidence implies that the high-Cr# chromitites were produced or emplaced in an earlier mature arc (possibly Jurassic), while the low-Cr# associations formed in an incipient forearc during the initiation of a new episode of Neo-Tethyan subduction at ~130–120 Ma. This two-episode subduction model can provide a new explanation for the coexistence of high- and low-Cr# chromitites in the same volume of ophiolitic mantle.