Intercalation compounds of anthraquinone sulfonate ions into layered double hydroxides (LDHs) have been directly synthesized. From the X-ray diffraction data and the guest size, the orientation of the intercalated anthraquinone sulfonate ions was determined. The intercalated anthraquinone-l,5-disulfonate (AQ15) and anthraquinone-2,6-disulfonate (AQ26) are arranged with their molecular planes and their sulfonate group axes tilted to the perpendicular of the hydroxide layer. Intercalated anthraquinone-2-sulfonate (AQ2) is arranged with the molecular plane and its sulfonate axis also perpendicular to the hydroxide layer with an antiparallel pattern. The product from a mixture of AQ2, AQ15 and AQ26 was also prepared; 86.8% of AQ2 and 13.2% of AQ26 were co-intercalated, whereas AQ15 was not intercalated into the LDH. These results indicate the possibility of a molecular recognition ability of LDH.