We successfully characterized the local structures of Bi atoms in a wire-δ-doped layer (1/8 ML) in a Si crystal, using wavelength dispersive fluorescence x-ray absorption fine structure at the beamline BL37XU, in SPring-8, with the help of density functional theory calculations. It was found that the burial of Bi nanolines on the Si(0 0 1) surface, via growth of Si capping layer at 400 °C by molecular beam epitaxy, reduced the Bi-Si bond length from [Formula: see text] to [Formula: see text] Å. We infer that following epitaxial growth the Bi-Bi dimers of the nanoline are broken, and the Bi atoms are located at substitutional sites within the Si crystal, leading to the shorter Bi-Si bond lengths.