The origin of growth defects and epitaxial layers in nanocrystalline magnetite (Fe₃O₄) and its oxidation product, maghemite (γ-Fe₂O₃), was studied. In magnetite, two types of planar defects are identified, (111) spinel-law twin boundaries and (110) stacking faults (SF). The twinning in magnetite is related to magnetic-field-assisted self-assembly and the growth of octahedral nanocrystals throughout their crystallization period. Simple contact twins of crystals sharing common octahedral faces, or even plate-like twins develop when two adjoined crystals continue their growth as a unit. Crystallographically, twinned domains are related by 180° rotation about the [111]-axis and with the (111) plane as the interface, producing local hcp stacking in the oxygen sub-lattice. SFs are present in both single and twinned magnetite crystals, where they are pinned to (111) twin boundaries and are present only in one domain. The displacement vector corresponding to the observed translation is R_SF = ¼·[110], pointing normal to the (110) plane of the SF. After the thermal treatment at 250 °C both types of planar defects are retained. In addition to planar defects, originating from magnetite, we identified a new formation of few-nanometers-thick epitaxial layers, of a hexagonal Fe(III)-oxide–hydroxide, feroxyhyte (δ-FeOOH), covering the octahedral faces of the maghemite crystals. The crystallographic relationship between maghemite and feroxyhyte is described by [10]·(222)_mag||[010]·(002)_fer.