Iron and silicon in various proportions are the major components of the newly formed hydrothermal sediments in the Atlantis II Deep, Red Sea. Iron-rich 2:1 phyllosilicates with morphologies varying from ribbons to plates represent clays in initial formation stage. Well-crystallized goethite particles contain domains of hundreds of nanometers in length with the rare presence of dislocations. Molar compositions show ratios of Si/Fe = 0.12 and Al/Fe = 0.05. Euhedral feroxyhyte with curled edges forms clusters with the goethite. The feroxyhyte has ratios of Si/Fe = 0.3 and are the major Si-associated iron oxides. Two nanometer-size phases showing short range periodity are common in the newly formed Atlantis II sediments: (1) hematite with traces of Si and (2) ferrihydrite with Si/Fe molar ratios varying between 0.17–0.89. The ferrihydrite forms large clusters. Hematite appears also as well-crystallized large crystals. Feroxyhyte probably forms at the transition zone between Red Sea Deep Water and the upper convective layer in the brine, whereas goethite and ferrihydrite form in the upper convective layer. The two forms of hematite represent two stages of recrystallization, which occur within the brine.