In order to understand the anti-site disorder effect on the anisotropic magnetoresistance (AMR) of alloys, Fe50Co50 alloys were studied in this work using the fully relativistic spin-polarized Korringa-Kohn-Rostoker (SPR-KKR) method. The anti-site disorder was modeled by interchanging Fe and Co atoms and treated by the coherent potential approximation (CPA). It is found that the anti-site disorder broadens the spectral function and decreases the conductivity. Our work emphasizes that the absolute variations of resistivity under magnetic moment rotation are less affected by atomic disorder. The annealing procedure improves the AMR by reduction of the total resistivity. At the same time, we also find that the fourth-order term in the angular dependent resistivity becomes weaker when the disorder increases, resulting from increased scattering of the states around the band-crossing.