In this study, we investigated the molecular characteristics of hydrates which were synthesized from gas mixtures containing the two isomers of butane, or the pentane isomers neopentane and isopentane, in excess methane. Thereto various techniques, including Raman spectroscopy, powder and single crystal X-ray diffraction and 13C NMR spectroscopy were employed. It turned out that shape and conformation of the guest molecule and hydrate structure both influence each other. In case of the mixed butane hydrate it could be confirmed that n-butane is enclathrated in its gauche conformation. This was verified by Raman spectroscopy, single crystal X-ray diffraction and calculated data. While isopentane is known as a structure H former, our results from powder X-ray diffraction, 13C NMR and ab initio calculations show that it can be also incorporated into structure II when the hydrate is formed from a neopentane/isopentane/methane gas mixture.