Selective ceramide (CER) subspecies CER[AP]-C18 and CER[EOS]-br and their partially deuterated variants were applied in stratum corneum (SC) lipid model membranes, in order to get closer insights into their molecular arrangement. For that purpose, multilamellar lipid membranes were investigated using neutron diffraction technique. CER[AP] was determined in a short-periodicity phase (SPP) as single CER component of a SC lipid model membrane. Together with CER[EOS]-br, three coexisting lipid phases were observed, in detail two SPP and one long-periodicity phase (LPP). CER[AP], again, was localized in both SPP, CER[EOS] was present in the LPP, which is highly connected to the SC barrier properties. Additionally, the impact of lipophilic penetration enhancer isopropyl myristate (IPM) on this model system was investigated. Here, no three coexisting phases were observed, but a single SPP. Within this SPP, both applied CER subspecies were determined.