Actively mined Carlin-type gold provinces are only found in Nevada, USA, and SW China. Herein, we combined nanoscale secondary ion mass spectrometry and atom probe tomography to characterize the distribution of Au and As in pyrite from the micrometer to atomic scales from the Shuiyindong and Lannigou deposits, SW China, and compared this with a representative Nevadan deposit. Results show that invisible gold in both deposits occurs in complex micrometer and nanometer scale zones in the rims of pyrite. Within these oscillatory zones, Au is homogenously distributed rather than occurring as nanoclusters. This confirms that invisible gold is principally structure-bound Au, and that ore fluids were not saturated in Au. Gold deposition from undersaturated, arsenic containing, and ore fluids led to the formation of the giant Carlin-type gold deposits. Although not all high-As zones in the Lannigou pyrite contain high Au, all high-Au zones in both deposits contain elevated As. Arsenic is an important criterion for the incorporation of Au, but just because the fluid had high As does not necessarily imply it had/precipitated a high-Au pyrite. Gold atoms, in the Au–As rich zones of pyrite from both deposits, are surrounded by elevated concentrations of As compared to the matrix. Therefore, As both promotes Au incorporation into the pyrite and controls the maximum amount of structure-bound Au in the pyrite. Comparison of the Guizhou pyrite with Nevada pyrite reflects that the pyrite from the two districts exhibits the consistent nanometer- to atomic-scale characteristics. These similar nanometer- to atomic-scale characteristics further support the Guizhou deposits being classed as “Carlin-type.”