The ϵ-Fe2O3 phase is commonly considered an intermediate phase during thermal treatment of maghemite (γ-Fe2O3) to hematite (α-Fe2O3). The routine method of synthesis for ϵ-Fe2O3 crystals uses γ-Fe2O3 as the source material and requires dispersion of γ-Fe2O3 into silica, and the obtained ϵ-Fe2O3 particle size is rather limited, typically under 200 nm. In this paper, by using a pulsed laser deposition method and Fe3O4 powder as a source material, the synthesis of not only one-dimensional Fe3O4 nanowires but also high-yield ϵ-Fe2O3 nanowires is reported for the first time. A detailed transmission electron microscopy (TEM) study shows that the nanowires of pure magnetite grow along  and <211> directions, although some stacking faults and twins exist. However, magnetite nanowires growing along the <110> direction are found in every instance to accompany a new phase, ϵ-Fe2O3, with some micrometer-sized wires even fully transferring to ϵ-Fe2O3 along the fixed structural orientation relationship, (001) ∥ (111),  ∥ <110>. Contrary to generally accepted ideas regarding epsilon phase formation, there is no indication of γ-Fe2O3 formation during the synthesis process; the phase transition may be described as being from Fe3O4 to ϵ-Fe2O3, then to α-Fe2O3. The detailed structural evolution process has been revealed by using TEM. 120° rotation domain boundaries and antiphase boundaries are also frequently observed in the ϵ-Fe2O3 nanowires. The observed ϵ-Fe2O3 is fundamentally important for understanding the magnetic properties of the nanowires.