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The Indian Ocean is a dynamically complex and highly variable system, with circulation features and biogeochemical properties that are unusual in many respects. Yet the Indian Ocean (IO) remains one of the most undersampled and least understood of the world's ocean basins. In this article, we define several outstanding research questions that need to be addressed in the IO related to ocean currents and variability, the controls and fate of primary production, global change and anthropogenic impacts, and the role of higher trophic levels in ecological processes and biogeochemical cycles. We also discuss a unique opportunity that has recently arisen for staging research in the IO.