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The effect of substrates on the microstructure and magnetic properties of electrodeposited Co nanowire arrays in porous anodic aluminum oxide membrane was investigated. It is found that the nanowires possess dominant (002) and (110) textures on the Co-coated nanocrystalline Finemet™ and Au substrates, respectively. Magnetic measurements show that the easy axis of the nanowire arrays switches from perpendicular to the wire axis on Au to parallel to the wire axis on the Co-coated nanocrystalline Finemet™ substrate.