The Durkan Complex in the Makran Accretionary Prism (SE Iran) has been interpreted either as a continental margin succession or a Late Cretaceous tectonically disrupted seamount chain. New whole rock and clinopyroxene chemical data for basaltic and metabasaltic rocks of the Durkan Complex allow us to distinguish two main rock groups: a) rocks showing transitional chemical affinity (Group 1) and compositions resembling those of plume-type mid-oceanic ridge basalts; b) rocks with within-plate oceanic island basalt (OIB) compositions showing a clear alkaline affinity (Group 2). Based on whole rock REE contents and clinopyroxene chemistry, alkaline rocks can be further subdivided in two sub-groups, namely, the Group 2a and 2b. Compared to Group 2a, Group 2b rocks show a more pronounced alkaline nature marked by higher whole rock La/Yb and Sm/Dy ratios and higher TiO2 and Na2O contents in clinopyroxenes. Trace element and REE petrogenetic models show that the Durkan basaltic rocks were generated from the partial melting of depleted sub-oceanic mantle source that was metasomatized by OIB-type chemical components in a within-plate oceanic setting. The chemical differences in the three rock groups are related to different combinations of partial melting degree, depths of melting, and various extent of enrichment of the mantle sources by OIB-type chemical components, which are related, in turn, to a Late Cretaceous mantle plume activity in the northern Neo-Tethys realm. We suggest that the Durkan Complex formed in a seamount setting and that its different volcano-sedimentary successions record different stages of seamount formation.