Provided are a molecular electronic device including a functional molecular active layer having a stack structure including oppositely charged first and second molecular active layers, and a method of manufacturing the molecular electronic device. The molecular electronic device includes: a first electrode; an organic dielectric thin layer comprising molecules each having a first end self-assembled on a surface of the first electrode and a second end having a cationic or anionic group; a functional molecular active layer stacked on the organic dielectric thin layer by selective self-assembly with positive and negative ions and comprising an electroactive functional group having a cyclic compound; and a second electrode formed on the functional molecular active layer.
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