Experimental results for methane and carbon dioxide diffusion in coal, as reported in the literature, often lead to diffusion rates of CO2 appearing to be much greater than that of CH4. The interpretation sometimes offered that the diffusion coefficient for CO2 is 1–2 orders of magnitude higher than that of CH4, violates fundamental principles. Nevertheless, the experimental observations require explanation. In this article, we: (a) Develop simplified models for the fast estimation of transport coefficients. These are compared with comprehensive grand canonical Monte Carlo (GCMC) and molecular dynamic (MD) simulations, collectively defined as molecular simulations (MS), which provide theoretical adsorption isotherms and various transport coefficients based on multicenter potential energy equations. The simplified models are shown to have acceptable accuracies. (b) Use the simplified models to compare diffusivities of CO2 and CH4 in carbon nanopores. For all cases examined, the diffusivity of CH4 is always larger than that of CO2. (c) Offer two explanations for the apparently contradictory experimental observations (that CO2 sometimes appears to diffuse much faster than the CH4 molecule, even though CH4 is lighter and has smaller adsorption affinity): (i) CH4 mobility could be significantly reduced by directional forces resulting from irregular pore geometries; and (ii) if pores contain throats with sizes close to the CH4 molecular diameter, the energy barrier that the methane molecules must overcome to proceed through is much larger than that required for CO2. (d) Demonstrate that both mobility and connectivity issues can be addressed using kinetic theory in association with percolation analysis. Furthermore, this method of understanding pore networks provides a number of important quantitative measures including percolation threshold, size of largest cluster, shortest path and tortuosity. Separating different transport mechanisms, as we propose here, provides improved insights into the complex transport phenomena that occur in carbonaceous porous media. In many cases, diffusivities reported in the literature with mixed mechanisms are better named “apparent transport coefficients,” because they lump in other unrelated phenomena, violating the fundamental basis of, or mathematical assumptions imposed on, the definition of diffusion. © 2011 American Institute of Chemical Engineers AIChE J, 2012