The correlation between the crystal structure and the magnetic properties of Co nanowires of diameter 65 and 200 nm fabricated by electroplating Co into the pores of anodic aluminum oxide membranes has been investigated. Strikingly different microstructures have been observed in these Co nanowires by means of x-ray diffraction and selected area electron diffraction measurements. The 65 nm thick Co nanowires are composed of long and ordered hexagonal close-packed Co grains (>5 microm), while the 200 nm thick Co nanowires are composed of submicron-long hexagonal close-packed and face-centered cubic Co grains. Correspondingly, different magnetic properties have been observed for these Co nanowires. Magnetization measurements have found that the 65 nm thick Co nanowires have a magnetic hysteresis that is significantly larger than that of the 200 nm thick Co nanowires. Spontaneous magnetic moments of the nanowires are parallel to the nanowires in the 65 nm thick Co nanowires, but they are transverse to the nanowires in the 200 nm thick Co nanowires, as observed by the magnetic force microscopy. The correlation between their different magnetic properties and microstructures is discussed.