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The insufficient data on a structure of the boron-doped diamond (BDD) has frustrated efforts to fully understand the fascinating electronic properties of this material and how they evolve with doping. We have employed X-ray diffraction and Raman scattering for detailed study of the large-sized BDD single crystals. We demonstrate a formation of boron-carbon (B-C) nanosheets and bilayers in BDD with increasing boron concentration. An incorporation of two boron atoms in the diamond unit cell plays a key role for the B-C nanosheets and bilayer formation. Evidence for these B-C bilayers which are parallel to {111} planes is provided by the observation of high-order, super-lattice reflections in X-ray diffraction and Laue patterns. B-C nanosheets and bilayers minimize the strain energy and affect the electronic structure of BDD. A new shallow acceptor level associated with B-C nanosheets at ~37 meV and the spin-orbit splitting of the valence band of ~6 meV are observed in electronic Raman scattering. We identified that the superconducting transitions occur in the (111) BDD surfaces only. We believe that the origin of Mott and superconducting transitions is associated with the two-dimensional (2D) misfit layer structure of BDD. A model for the BDD crystal structure, based on X-ray and Raman data, is proposed and confirmed by density functional theoretical calculation.Electronic supplementary materialThe online version of this article (doi:10.1186/s11671-015-1215-6) contains supplementary material, which is available to authorized users.