Abstract Atomistic structures of high-fluence Mn ion implanted Si were examined using transmission electron microscopy (TEM). Si(0 0 1) single crystals were irradiated at cryogenic temperature with 120 keV Mn ions to a fluence of 3.0 × 10 17/cm 2. Cross-sectional TEM observations revealed that an amorphous bilayer consisting of amorphous Mn–Si and amorphous Si is formed on the topmost layer of the Si substrate. Atomic pair-distribution functions extracted from electron diffraction patterns indicated that short-range order of the amorphous Mn–Si thin layer is similar to the local atomic configuration of higher manganese silicides. The amorphous Mn–Si layer crystallized to Mn 4Si 7 polycrystalline layer by thermal annealing.