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Co nanowire arrays of different crystal structures have been electrodeposited into self-assembled anodic aluminum oxide (AAO) templates by varying pH value of electrolyte. The XRD results show that crystal structure of Co nanowires is fcc structure at pH = 2.5, a mixed structure of fcc and hcp at pH = 3.0 and 3.5, and hcp structure at pH =5.0. Magnetic measurements indicate that Co nanowire arrays of different crystal structures exhibit different magnetic properties. The coercivity of Co nanowire array of fcc structure is larger than that of hcp structure about 900 × 103/4πA · m-1 along wire axis, and its squareness is also larger than that of hcp structure.