Cobalt nanowire arrays have been grown onto anodic aluminum oxide templates by using a pulse dc electrodeposition technique. We demonstrate that the crystal structure, grain size, and related magnetic properties can be controlled by applying different pulse frequencies. For a pulse frequency of 25 Hz, monocrystalline hexagonal-close-packed Co nanowires are formed with a well defined [10 1- 0] growth axis along the wire length. At a higher pulse frequency of 1000 Hz, face-centered-cubic Co nanowires are deposited with a small grain size and a preferred  texture directed along the length of the wire. Possible mechanisms for the observed growth characterization are discussed. An investigation of the corresponding magnetic properties indicates that the fcc Co nanowire arrays have the larger coercivity and squareness values: reasons for this behavior are explored.