Plasma polymer films prepared from perfluoro-2-butyltetrahydrofuran (PFBTHF) and perfluorobenzene (PFB) were investigated by elemental analysis, infrared spectroscopy, and ESCA. The gas separation properties were also investigated to seek plasma polymer films with good permselectivity. Plasma polymer films from PFBTHF and PFB were composed of polymer chains with fluorinated moieties such as C–CFn, CF, CF–CFn, CF2, and CF3 groups. Changes in the afcurrent as an operating condition for plasma polymerization showed less influence on the distribution of the fluorinated moieties but more influence on the permselectivity of the plasma polymer films formed. The permselectivity was improved by plasma polymerization in the PFBTHF/CH4 or PFB/CF4 mixture systems. The PO2/PN2 ratio for the plasma polymer films prepared from PFBTHF/CH4 and PFB/CF4 mixtures increased from 3.1 at 0 mol % CH4 to 4.0 at 50 mol % CH4 addition, and from 4.1 at 0 mol % CF4 to 5.0 at 25 mol % CF4 addition, respectively. The permselectivity of the plasma polymer films may be related to the crosslinkage and aggregation of polymer chains rather than the elemental composition.