Magnetic Co-Cr nanowire arrays with different Cr contents were successfully synthesized in an anodic aluminum oxide (AAO) template by alternating current(AC) electrodeposition. The effects of Co and Cr composition, electrodeposition conditions (frequency and voltage) and annealing on magnetic and structural properties of the produced nanowires were investigated. The results demonstrated that coercivity (Hc) of nanowires increased with increasing Cr concentration. Also, the squareness of prepared nanowires improved when the Cr content reached to 7.5 %. Also, the coercivity of Co92.5Cr7.5 nanowire improved after thermal annealing at 650◦C. Hysteresis loops measured for the synthesized nanowires at different electrodeposition frequencies exhibit higher coercivity and squareness for nanowires prepared at 200 Hz. Meantime, magnetic properties of the nanowires were seen to be independent of electrodeposition voltage. The effect of sulfates and chlorides counter ions of Co+2 and Cr+3 in the electrolyte solution on magnetic properties of prepared Co-Cr nanowires was investigated.