The sequential application of mild and hard anodization techniques in the fabrication of porous alumina membranes allows one to decrease the number of continuous pores in anodized aluminium oxide (AAO) templates. Initially, standard mild anodization techniques were used to create porous templates with 100 nm interpore distances and 70 nm pore diameters. Hard anodization treatment on the same membrane then produced interpore distances of about 265 nm with diameters of 110 nm. At the interface between the two anodization steps, many of the mild-side pores were terminated to create a mild–hard membrane (Mi–Ha AAO) where the functional interpore distances were 200–300 nm. Growth (electrodeposition) of nickel and cobalt nanowires in the various pore structures of the mild and hard sides of the Mi–Ha AAO templates allows one to probe magnetic interactions between nanowires and compares them to wires grown in standard mild templates (Mi-AAO). The magnetic properties of nanowires in Mi–Ha AAO and Mi-AAO showed distinct differences in the squareness of hysteresis loops and coercivity both as a function of pore structure and magnetic component. In general, the squareness of the hysteresis loops increased with aspect ratio and greater interpore distance. Coercivity also showed an increase with aspect ratio, but varied differently with interpore distance for Ni and Co. These various magnetic behaviors are discussed with respect to crystalline structure, morphology, and interactions of adjacent sets of nanowires.