The volcanic section of the Manipur Ophiolite (MO), representing the crustal portion of the Neo-Tethyan oceanic lithosphere occurs as basalt, basaltic trachyandesite, and dacite in the Gamnom-Phangrei sector, Manipur, at 25°01′N–25°09′N and 94°24′E–94°27′E. They associate with cherts and ultramafics. The clinopyroxene compositions of basalt and basaltic trachyandesite, obtained through electron microprobe analyzer, were used as a petrogenetic indicator to identify the parent magma-types and their tectonic settings. Based on the variable content of major oxides, they are classified as high- and low-Ti clinopyroxenes. High Ti and Al contents with relatively lower silica saturation are observed in the former group and vice versa in the latter. The TiDCpx/rock values in low- and high-Ti clinopyroxene are comparable with island-arc basaltic andesite and MORB, respectively, which confirms that the clinopyroxene composition is primarily related to the host magma-type and its tectonic setting. Clinopyroxene thermometry (ranging 1150–605 °C) suggests progressive differentiation of the parent magmas. Several bivariate and tectonic discrimination diagrams depict MORB (non-orogenic setting) and island-arc boninitic magma affinities (orogenic setting) for the high- and low-Ti clinopyroxenes, respectively. The coexistence of both MORB and island-arc boninitic magma-types in the volcanic section of Manipur Ophiolite as characterized by their varying Ti, Al, and Si contents may indicate either juxtaposition of rocks formed in diverse tectonic settings (i.e., due to transformation of tectonic setting from mid-ocean ridge to supra-subduction zone) or, a change in magma composition in a subduction zone setting. However, field relationships coupled with the mineral–chemical signatures implies a supra-subduction zone setting for the evolution of the crustal section of MO. © 2017, Springer-Verlag GmbH Germany.