The negative uniaxial magnetocrystalline anisotropy (Ku) was evaluated for various compositions of Co100-xIrx thin films with respect to the atomic layer stacking structure. Pure Co film fabricated at a substrate temperature (Tsub) of 600 C was found to have a positive Ku of 6.1×10 6 erg/cm 3 . With increasing x, the sign of Ku changed from positive to negative, and the negative Ku took a maximum value of -9.6×10 6 erg/cm 3 at around x = 20 at. % for films fabricated at Tsub = 600 C. Adding more Ir decreased the absolute value of the negative Ku which became 0 over x = 50 at. %. X-ray diffraction analysis and scanning transmission electron microscopy revealed that the atomic layer stacking structure of the Co100-xIrx films changed from -A-B-A-B-(hcp) to -A-B-C-A-B-C-(fcc) stacking with increasing Ir content. Moreover, Co80Ir20 grains were revealed to consist of 2 kinds of randomly located composition-modulated atomic layers, nearly pure-Co and pure-Ir layers, while Co and Co50Ir50 had disordered structures. In this paper, a new perspective on the atomic layered structure with superlattice diffraction, which is different from the conventional "ordered structure", is discussed.