Maya blue paint was often used in Mesoamerica. The origin of its color and its resistance to acids and biocorrosion have not been fully understood. High-resolution transmission electron microscopy, electron energy loss spectroscopy, and x-ray microanalysis studies of authentic samples show that palygorskite crystals in the paint form a superlattice that probably occurs as a result of mixing with indigo molecules. An amorphous silicate substrate contains inclusions of metal nanoparticles encapsulated in the substrate and oxide nanoparticles on the surface. The beautiful tone of the color is obtained only when both the particles and the superlattice are present.