In the present work, equiatomic FeNi and FeCo magnetic nanowires (NWs) have been electrodeposited in Anodic Aluminum Oxide (AAO) membranes with 70 nm pore size. The role of the electroactive species Ni2+ and Co2+ on the anomalous codeposition behavior in thin films and nanowires has been discussed and compared. Field Emission Gun-Scanning Electron Microscope (FEG-SEM), X-ray diffraction (XRD) and Vibrating Sample Magnetometer (VSM) were used to evaluate the morphology, composition, crystalline structure and magnetic properties of the materials. SEM-FEG analysis showed very homogeneous NWs lengths for both FeNi and FeCo NWs, Energy dispersive X-ray spectroscopy (EDS) analysis revealed a stable composition along the FeCo NWs and a change in composition along the FeNi NWs. The XRD patterns indicate the predominance of the bcc structure for both alloys. Except for additional peaks of fcc phase found on FeNi alloy, the same crystalline bcc structure is observed after annealing treatment of 300 °C during 20 h. TEM analysis confirmed the ordered character of the bcc FeCo alloy. The hysteresis loops show an easy magnetization direction parallel to the wires due to the predominance of the shape anisotropy. The coercive field (Hc) of FeNi NWs increases with the length of the wires while that of FeCo NWs decreases. The annealing treatment doesn’t affect the magnetic properties of FeNi NWs, whereas a remarkable increase in the coercivity of the FeCo NWs is observed.