We report the formation of aggregated thionine molecules encapsulated within an Al-containing mesoporous molecular sieve material (specifically, AIMCM-48) that possesses a cubic pore structure. XRD, UV-vis absorption, fluorescence, and Raman measurements were used, where appropriate, as spectroscopic tools to characterize the AIMCM-48 host sample and the composite system consisting of the host and encapsulated thionine molecules. Due to the size of the cubic pores possessed by the host, aggregates of thionine larger than the dimers, trimers, and so forth, reported hitherto, are likely formed and are more appropriately termed H-aggregates. The structure of the H-aggregate is proposed. Raman band assignments for thionine are made based on both empirical determinations and quantum chemical calculations using density functional theory at the B3LYP level.