There are conflicting reports on molecular interactions between indigo and the members of the palygorskite family (natural porous clays) both components of the famous Maya Blue pigment. For indigo molecules and sepiolite, a clay of the palygorskite family, we have recently reported a synthesis to introduce indigo in intracrystalline channels and show that it is possible to replace a large part of the zeolitic water in sepiolite using indigo molecules . Now, in addition, we find evidence for two complex forms of indigo-sepiolite. The first is due to H-bonding interactions between indigo and magnesium coordinated water (indigo is in a sepiolite tetrahydrate environment (SEP4H2O-Id)); the second is due to direct interactions between Mg2+ cations and indigo (indigo is in a sepiolite dihydrate environment (SEP2H2O-Id)). These two blue complexes have small differences in shade ranges. It should be stressed that the formation of complexes of the sepiolite dihydrate is reversible; in the presence of water, the sepiolite tetrahydrate complex is formed again. The same types of complexes are observed for indigo-palygorskite systems. However, in contrast to sepiolite, the dihydrate palygorskite complex remains stable at air for months instead of weeks. Finding evidence to support the formation and control of complexes related to these organic-inorganic nanohybrids is a particularly interesting task because the identification of new properties in these nanocomposites enhances their potential for use in actual application.