Fluorine containing polymers are of special interest because of their possible use as gas selective membranes, their remarkably low water absorption and their low dielectric constant and enhanced flame resistance. In this work, the gas transport and separation properties of H-2, CO2, O-2, N-2 and CH4 were studied for four novel poly(arylene ether)s (PAEs) membranes, two containing the 2,6-bis(trifluoromethylphenylene)pyridine unit (6FPPy series) and the others containing 2,5-bis(3-trifluoromethylphenylene)thiophene unit (6FPT series) in the polymer backbone. The preparation of this new class of semifluorinated polymers relied on the aromatic substitution polymerization of trifluoromethyl activated bishalo monomers with different bis(phenol)s. It was found that the introduction of -CF3 groups into the bisphenol unit increases the gas permeabilities and decreases slightly the selectivities for both series of membranes. The gas permeability coefficients of 6FPPy membranes are higher than those of 6FPT membranes while their selectivities are comparable. These results were discussed based on the gas diffusion and solubility in the membranes and could be ascribed to the polymer structure. The effect of temperature on the gas transport properties of these membranes was measured and the corresponding activation energies for gas permeation and diffusion were calculated.