The structure of the indigo@silicalite pigment, an analog of ancient Maya Blue, has been determined by combining X-ray Laue microdiffraction and powder diffraction techniques. After the adsorption of indigo into the calcined (monoclinic) silicalite sample, the powder diffraction pattern contained peaks from both orthorhombic (major phase) and monoclinic (minor phase) silicalite. Assuming that the orthorhombic phase was induced by the adsorption of indigo, Laue microdiffraction was used to map the unit cell changes (and thereby the indigo distribution) within a single crystal. It was found to be highly heterogeneous with empty monoclinic and indigo-induced orthorhombic domains. The Laue diffraction data indicated that the space group of the orthorhombic domains was Pnma rather than P212121. With this information, the indigo@silicalite structure could be solved and refined from the powder diffraction data. The starting positions for two independent indigo molecules, described as rigid bodies, were obtained by simulated annealing, with a first molecule positioned in the straight channel and the second one in the sinusoidal channel. The positions and occupancies of these molecules and the positions of the framework atoms were then refined using the Rietveld method. Approximately four indigo molecules per unit cell were found, two per independent site, and possible local arrangements are suggested. The size of the indigo molecule prevents the structure from being fully ordered.