Abstract Arrays of epitaxial Fe₃O₄ nanodots were prepared using laser molecular beam epitaxy (LMBE), with the aid of ultrathin porous anodized aluminum templates. An Fe₃O₄ film was also prepared using LMBE. Atomic force microscopy and scanning electron microscopy images showed that the Fe₃O₄ nanodots existed over large areas of well-ordered hexagonal arrays with dot diameters (D) of 40, 70, and 140 nm; height of approximately 20 nm; and inter-dot distances (D _int) of 67, 110, and 160 nm. The calculated nanodot density was as high as 0.18 Tb in.⁻² when D = 40 nm. X-ray diffraction patterns indicated that the as-grown Fe₃O₄ nanodots and the film had good textures of (004) orientation. Both the film and the nanodot arrays exhibited magnetic anisotropy; the anisotropy of the nanoarray weakened with decreasing dot size. The Verwey transition temperature of the film and nanodot arrays with D ≥ 70 nm was observed at around 120 K, similar to that of the Fe₃O₄ bulk; however, no clear transition was observed from the small nanodot array with D = 40 nm. Results showed that magnetic properties could be tailored through the morphology of nanodots. Therefore, Fe₃O₄ nanodot arrays may be applied in high-density magnetic storage and spintronic devices.