Abstract The host phase of iodine (I) in biogenic iron oxyhydroxides (BIOS) was determined using X-ray absorption near-edge structure (XANES). I K-edge and LIII-edge XANES analyses of BIOS collected from deep-sea hydrothermal environments revealed that the primary form of I in the BIOS is an organic species. Furthermore, LIII-edge XANES fitting implied the dominance of aromatic-bound I among BIOS. Our first observation of organic–trace element association in natural BIOS can explain the enhanced adsorption of I on BIOS compared to synthetic ferrihydrite. This further suggests the importance of various chemistry on this organic–mineral composite for understanding the geochemical cycling of trace elements.