Deep sediments from the Red Sea have been studied extensively and provide a rich resource for understanding mineral transformations under hydrothermal conditions. Interrelationships among various sampling sites, however, are still rather incomplete. The purpose of the present study was to increase understanding of these systems by characterizing and comparing the Fe-Mn oxyhydroxides from the southern Atlantis II, Chain A, Chain B, and Discovery Deeps, using high-resolution transmission electron microscopy. Some of the hydrothermal sediments of Chain A are dominated by Si-associated Fe oxides (ferrihydrite, goethite, lepidocrocite, and short-range ordered, rounded particles) resembling the hydrothermal sediments of the SW basin in the Atlantis II Deep, indicating sub-bottom connections between the Deeps. Although some of the sediments of the Discovery Deep show a similar trend; short-range ordered, rounded particles were not detected in these sediments, implying that crystallization of this short-range ordered phase is sensitive to the Si/Fe ratio in the brine and only at elevated ratios does it crystallize out of the brine. Silicon-associated and Fe-enriched Mn oxyhydroxides such as groutite, manganite, todorokite, and Mn-dominated lathlike layers occasionally contain Ca and Mg impurities. Manganese substitutes for Fe and vice versa, leading to a solid-solution series between goethite and groutite and Mn-enriched ferrihydrite. Hematite is the only Fe oxide in the hydrothermal sediments that is found to be lacking in impurities, which is probably due to its formation by recrystallization from other Fe oxides.