Co49Pt51 nanowire arrays with an average diameter of 35 nm and lengths up to several micrometers were grown in an ordered porous anodic aluminum oxide (AAO) template using direct-current electrodeposition. The as-deposited samples were annealed at 100, 200, 300, 400, 500, 600, and 700 degreesC, respectively. The temperature dependence of the magnetic property of the Co49Pt51 nanowire arrays associated with the microstructure was analyzed by X-ray diffraction and a vibrating sample magnetometer. Magnetic measurements show that the samples both as-prepared and annealed at low temperatures have excellent perpendicular anisotropy. The perpendicular coercivity (H-cperpendicular to) of Co49Pt51 alloy nanowire arrays increases dramatically as the annealing temperature (T-A) rises, reaches a maximum(H-cperpendicular to = 2770 Oe) at 400 degreesC, and then decreases sharply as T-A rises further. This phenomenon should be attributed to the special structure of the nanowire arrays/AAO, and the microstructure factors significantly change during the annealing process.