The worldwide increase of graphene family materials raises the question of the potential consequences resulting from their release in the environment and future consequences on ecosystem health, especially in the aquatic environment in which they are likely to accumulate. Thus, there is a need to evaluate the biological and ecological risk but also to find innovative solutions leading to the production of safer materials. This work focuses on the evaluation of functional group-safety relationships regarding to graphene oxide (GO) in vivo genotoxic potential toward X. laevis tadpoles. For this purpose, thermal treatments in H2 atmosphere were applied to produce reduced graphene oxide (rGOs) with different surface group compositions. Analysis performed indicated that GO induced disturbances in erythrocyte cell cycle leading to accumulation of cells in G0/G1 phase. Significant genotoxicity due to oxidative stress was observed in larvae exposed to low GO concentration (0.1 mg.L−1). Reduction of GO at 200 °C and 1000 °C produced a material that was no longer genotoxic at low concentrations. X-ray photoelectron spectroscopy (XPS) analysis indicated that epoxide groups may constitute a good candidate to explain the genotoxic potential of the most oxidized form of the material. Thermal reduction of GO may constitute an appropriate “safer-by-design” strategy for the development of a safer material for environment.