The character of magmatism associated with the early stages of subduction zone and island arc development is unlike that of mature systems, being dominated in the Izu-Bonon-Mariana (IBM) case by low-Ti-K tholeiitic basalts and boninites. Basalts recovered by coring the basement of the Amami Sankaku Basin (ASB), located west of the oldest remnant arc of the IBM system (Kyushu-Palau Ridge; KPR), were erupted at ~49 Ma, about 3 million years after subduction inception. The chain of stratovolcanoes defined by the KPR is superimposed on this basement. The basalts were sourced from upper mantle similar to that tapped following subduction inception, and represented by forearc basalt (FAB) dated at ~52-51 Ma. The mantle sources of the ASB basalt basement were more depleted by prior melt extraction than those involved in the vast majority of mid-ocean ridge (MOR) basalt generation. The ASB basalts are low-Ti-K, aluminous spinel-olivine-plagioclase-clinopyroxene-bearing tholeiites. We show this primary mineralogy is collectively distinct compared to basalts of MOR, backarc basins of the Philippine Sea Plate, forearc, or mature island arcs. In combination with bulk compositional (major and trace element abundances plus radiogenic isotope characteristics) data for the ASB basalts, we infer the upper mantle involved was hot (~1400oC), reduced, and refractory peridotite. For a few million years following subduction initiation, a broad region of mantle upwelling accompanied by partial melting prevailed. The ASB basalts were transferred rapidly from moderate pressures (1-2 GPa), preserving a mineralogy established at sub-crustal conditions, and experienced little of recharge-mix-tap-fractionate regimes typical of MOR or mature arcs.