Highly ordered Co-Ag alloy nanowire arrays embedded in the nanochannels of anodic alumina membranes (AAMs) were successfully fabricated using electrodeposition. Scanning electron microscopy and transmission electron microscopy observations revealed that the ordered Co-Ag alloy nanowires were uniformly assembled into the hexagonally ordered nanochannels of the AAMs. Magnetic measurements showed that the perpendicular coercivity (Hc⊥) of the ordered nanowire arrays increased dramatically as the annealing temperature (Ta) rose from 300 °C, reached its maximum (183 Oe) at 400 °C and then decreased sharply as Ta further increased beyond 400 °C. However, there was little change in the parallel coercivity (Hc∥) of the nanowire arrays during the annealing process. The mechanism of this phenomenon was attributed to the special structure of the AAMs and nanowires.