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abstract: 'Clusters of galaxies have not yet been detected at gamma-ray frequencies; however, the recently launched Fermi Gamma-ray Space Telescope, formerly known as GLAST, could provide the first detections in the near future. Clusters are expected to emit gamma rays as a result of (1) a population of high-energy cosmic rays fueled by accretion, merger shocks, active galactic nuclei and supernovae, and (2) particle dark matter annihilation. In this paper, we ask the question of whether the Fermi telescope will be able to discriminate between the two emission processes. We present data-driven predictions for the gamma-ray emission from cosmic rays and dark matter for a large X-ray flux limited sample of galaxy clusters and groups. We point out that the gamma-ray signals from cosmic rays and dark matter can be comparable. In particular, we find that poor clusters and groups are the systems predicted to have the highest dark matter to cosmic ray emission ratio at gamma-ray energies. Based on detailed Fermi simulations, we study observational handles that might enable us to distinguish the two emission mechanisms, including the gamma-ray spectra, the spatial distribution of the signal and the associated multi-wavelength emissions. We also propose optimal hardness ratios, which 