Carbon molecular sieve membranes (CMSMs) are emerging as promising solution to overcome the drawbacks of Pd-based membranes for H2 separation since (i) they are relatively easy to manufacture; (ii) they have low production and raw material costs; (iii) and they can work at conditions where polymeric and palladium membranes are not stable. In this work CMSMs have been investigated in pure gas and gas mixture tests for a proper understanding of the permeation mechanism, selectivity and purity towards hydrogen. No mass transfer limitations have been observed with these membranes, which represents an important advantage compared to Pd-Ag membranes, which suffer from concentration polarization especially at high pressure and low hydrogen concentrations. H2, CH4, CO2 and N2 permeation at high pressures and different temperatures in presence of dry and humidified stream (from ambient and water vapour) have been carried out to investigate the effect of the presence of water in the feed stream. Diffusion is the main mechanism observed for hydrogen, while methane, nitrogen and especially carbon dioxide permeate through adsorption-diffusion at low temperatures and high pressures. Finally, H2 permeation from H2-CH4 mixtures in presence of water has been compared at different temperatures and pressure, which demonstrates that water adsorption is an essential parameter to improve the performance of carbon molecular sieve membranes, especially when working at high temperature. Indeed, a hydrogen purity of 98.95% from 10% H2—90% CH4 was achieved. The main aim of this work is to understand the permeation mechanisms of CMSMs in different operating conditions and find the best conditions to optimize the separation of hydrogen.