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By utilizing spin-polarized scanning tunneling microscopy (STM) and spectroscopy, we observe the coexistence of perpendicularly and in-plane magnetized cobalt nanoscale islands on an Ag(111) surface. The magnetization direction has the relationship with the observed moiré-corrugation amplitude on the islands; the islands with stronger moiré corrugation show perpendicular magnetization, and the ones with weaker moiré corrugation exhibit in-plane magnetization. We calculate the magnetic anisotropy energy for various stackings of a Co nanostructure based on density functional theory, and we reveal that perpendicular magnetic anisotropy is reduced drastically with increasing fcc stacking faults in the Co layer. Simulated STM images reproduce the moiré-corrugation difference observed experimentally when the stacking difference between perpendicularly and in-plane magnetized islands is considered …