A combined single-crystal X-ray diffraction (XRD) and FTIR study was performed to define the structures of SAPO-34 and CoAPSO-34 microporous molecular sieves synthesized using morpholine (C4H8ONH) as a structure-directing agent and to shed some light on the molecular interactions between molecules embedded within the zeolitic cages after hydrothermal synthesis. All investigated crystals showed a chabasite-related structure that was analyzed in the R-3 space group. The incorporation of Si and Co ions into the aluminophosphate framework was assessed by different procedures (scattering curve refinements and analysis of T-O distances). Silicon-to-phosphorus substitution was within the range of 20-24% Si in the P sites of all SAPO-34 crystals. Conversely, Si-for-P and Co-for-Al substitutions spanned a wider range in CoAPSO-34 crystals. XRD supplemented by TGA analysis showed that 2 morpholine and 2.5-3 water molecules occupied the chabasite cages in all crystals. The presence of morpholinium, C4H 8ONH2+ (HM+), along with morpholine (M) H-bonded to water molecules was detected by FTIR spectroscopy, and a computational study helped to clarify the assignment of the vibrational modes of the isolated organic molecules. The structure of water/morpholinium (or morpholine) molecular complexes, which are formed by HM+-H 2O-HM+ (or HM+-H2O-M) units within the chabasite cages and HM+-H2O-H2O-HM + (or HM+-H2O-H2O-M) chains embedded in the intrazeolite space of adjacent cages of the chabasite network, was refined by single-crystal XRD.