In this paper, we report preparation and structure determination of two new adeninium-based hybrid compounds formed with selenious acid: adeninium hydrogen diselenite (I) and adeninium hydrogen selenite (II). Single crystals of (I) and (II) were obtained by slow evaporation and their X-ray structures are reported coupled with a quantum chemical density functional theory (DFT) studies. In the atomic arrangement, the different entities are held together throughhydrogen bonds on the Watson−Crick, Hoogsteen and sugar sites. Their overall three-dimensional architectures are mostly controlled by electrostatic interactions between the inorganic anion and organic cation frameworks and by hydrogen bonding. Furthermore, the crystal structures of (I) and (II) contain supramolecular homo and heterosynthons which are present in most similar structures. The similarities and subtle differences of the intermolecular interactions in the two crystal structures have been investigated and discussed using Hirshfeld surface analysis, fingerprint plots, and contact enrichment. The theoretical results are in good relation with the experimental structural analysis and confirm that the charge transfer occurs from inorganic anions to organic cations.