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Abstract Iron (Fe) in seawater is an essential micronutrient for marine phytoplankton, and Fe deficiency limits their growth in high-nutrient, low-chlorophyll areas. The bioavailability of Fe for phytoplankton largely depends on its chemical speciation in seawater. In surface water, the reduction of Fe(III) to Fe(II) is an important step in the uptake of Fe by phytoplankton. However, the marine biogeochemical cycle of Fe(II) in the open ocean has not been fully investigated. In oxic open-ocean waters, Fe(II) is rapidly oxidized and exists at sub-nanomolar levels, making it difficult to determine the Fe(II) concentration of seawater. In this study, we applied the flow analytical method of determining the Fe(II) concentration of seawater using luminol chemiluminescence in an in-situ analyzer (geochemical anomaly monitoring system, GAMOS). In the onboard laboratory, we successfully detected sub-nanomolar levels of Fe(II) in seawater using the GAMOS. In the central Indian Ocean, this analyzer was deployed at a depth of 1000 m to determine the Fe(II) concentration in the water column. During deployment, the detection limit (0.48 nM) was insufficient to determine the concentration. Therefore, we need to lower the blank values and enhance the stability of signal of the in-situ analytical method for application to open-ocean seawater samples. Graphical abstract