We investigated benthic foraminiferal species as tracers for carbon export flux in the Indo-Pacific warm pool (International Ocean Discovery Program Expedition 363). In core tops, the distribution of lower bathyal and upper abyssal species can be separated into two distinct groups. Foraminifera belonging to the high carbon flux (>3.5 g C m−2 year−1), ‘warm’ (>3.5°C) group are Bolivina robusta, Bulimina aculeata, Globobulimina pacifica, Hoeglundina elegans, Laticarinina pauperata, and Cibicidoides pachyderma. The lower carbon flux, ‘cold’ group includes Oridorsalis umbontus, Uvigerina bifurcata, and Planulina wuellerstorfi. An index based on the percent ‘warm’ assemblage with respect to the total ‘warm’ plus ‘cold’ species in core-top samples correlates significantly with carbon flux (r = 0.91, P = 0.0007) and modern bottom water temperatures (r = 0.94, P = 0.0002). When applied to down-core species abundances based on core catchers spanning the late Miocene through Pleistocene, we observed that sites from the northwestern Australian margin show marked changes in the ‘warm’ index, suggesting a large paleoenvironmental signal in this dynamic region. At Papua New Guinea, down-core abundances of the ‘warm’ group are highest (>80%), consistent with high organic matter input via the Sepik River. At the deeper of the two sites, down-slope movement in this tectonically unstable region may have contributed to organic matter input. At Manus Basin, the ‘warm’ species abundances are also relatively high and covary with the percent abundance of Uvigerina proboscidea, providing further evidence for the use of this index as a tracer for carbon flux. Overall, this study contributes evidence for the relationship between benthic foraminiferal assemblages and carbon export flux in the Indo-Pacific warm pool, suggesting that the ‘warm’ index can be used as a tracer for paleoproductivity.