Todorokite is considered to form from vernadite in nature and commonly concentrates nickel. However, this mineralogical transformation has never been imaged nor explained mechanistically, and its effect on the uptake of nickel has never been quantified at the molecular-level. We have characterized these reactions at the macroscopic, microscopic, nanoscopic and atomic scales in a marine manganese concretion by combining transmission electron microscopy, electron and X-ray microprobe analysis, powder and micro X-ray diffraction, and Mn and Ni K-edge EXAFS spectroscopy. The concretion was collected during the Ticoflux II expedition near the Nicoya Peninsula, Costa Rica, and is representative of Mn deposits in hemipelagic sediments. It consists of 5 to 25 μm aggregates, shaped like sea-urchins, with a core of 7Å-vernadite (1.0 wt% Ni), a rim of 10Å-vernadite (3.8 wt% Ni), and an outermost region of todorokite fibers (1.9 wt% Ni) that extend outwards. The crystallites of 7Å-vernadite are single- to bi-layered, with hexagonal layer symmetry (a = b = 2.83 Å), and an average structural formula of View the MathML source. The crystallites of 10Å-vernadite contain 10 to 20 layers semi-coherently stacked in the ab plane and uniformly separated in the [0 0 1] direction by not, vert, similar9 Å due to the intercalation of hydrated Mg2+ cations. The average structural formula of 10Å-vernadite is View the MathML source if the layers contain vacancy sites, or alternately View the MathML source, if they contain Mn3+. The average formula of todorokite is View the MathML source. A genetic model is proposed based on combining these new data with previously published results. The thermodynamically unstable 7Å-vernadite transforms via dissolution-recrystallization to semi-ordered Mg-rich 10Å-vernadite. Nickel is released from dissolved biogenic silica or reduced organic matter, and taken up mainly in the Mn layer of 10Å-vernadite. Interlayer magnesium serves as a template to the further topotactic transformation of 10Å-vernadite to todorokite. The dimension of the todorokite tunnels in the [0 0 1] direction is uniform and determined by the size of the hydrated Mg2+ ion (8.6 Å). The tunnel dimension in the [1 0 0] direction depends on the density of Mg2+ in the interlayer and the superstructure of the phyllomanganate layer. If the parent phyllomanganate contains high amounts of Mg2+ (i.e., high layer charge), or Mn3+ and Mn4+ cations ordered following the Mn3+–Mn4+–Mn4+ sequence as in synthetic triclinic birnessite, then the tunnel dimension is ideally 3 × 3 octahedral chain widths in both crystallographic directions. Otherwise, the tunnel dimension is incoherent in the [1 0 0] direction (i.e., T(3,n) tunnel structure), as has been observed in all natural todorokites. Natural todorokite is defective because the precursor natural phyllomanganates either have a layer charge deficit below 0.33e per octahedral site, or rarely are triclinic birnessite. The abundance of Mg in seawater and its key role in converting phyllomanganate to tectomanganate with T(3,n) tunnel structure explain why todorokite is common in marine ferromanganese oxides, and seldom present in terrestrial environments. The topotactic phase transformation described here is the only known route to todorokite crystallization. This implies that all natural todorokites may be authigenic because they are formed in situ from a phyllomanganate precursor.