Phytoplankton growth in the upper sunlit ocean drives the oceans' biological carbon pump, a collection of processes that sequester atmospheric CO2 into the deeper ocean where it is stored for centuries to millennia. However, a large fraction of carbon does not reach greater depths but is respired by bacteria and other microorganisms as it sinks. Earlier field work found that, for water temperatures between 2 and 17°C, warmer water is associated with more carbon respiration. However, we observe that carbon respiration in the Gulf of Aqaba, a deep warm water body in the northern Red Sea, is much less intense than expected based on water temperature (≥20°C). Moreover, the local ecosystem exports a considerable fraction of carbon to intermediate depths (∼300–570 m). These results question the universal role of temperature in regulating carbon export in the ocean. They also suggest that ecosystems dominated by small phytoplankton can support considerable carbon export despite warm temperatures, especially when mineral dust is available to enhance the sinking of marine particles.

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