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Nowadays, biologically oxidizing graphitic materials is of great importance for practical applications as an eco-friendly and low-cost method. In this work, a bacterial strain is isolated from the contaminated soil in a graphite mine and its ability to oxidize graphite, graphene oxide (GO) and reduced graphene oxide (RGO) is confirmed. After being cultivated with bacteria, graphite is inhomogeneously oxidized, and moreover oxidized sheets exfoliated from graphite are detected in the medium. RGO shows a higher degree of oxidation compared to graphite owing to more original defects, while GO breaks into small pieces and becomes full of holes. Both the holes in GO and the exfoliated sheets from graphite caused by bacteria have a size of below 1 μm, in agreement with the size of bacterial cells. Besides, the preliminary mechanism of the bacterial oxidation is explored, suggesting that the contact between bacterial cells and materials promotes the oxidation of graphitic materials. The ability of naphthalene-degrading bacteria to oxidize and degrade the graphitic materials shows the potential for producing GO in an eco-friendly way and degrading carbon nanomaterials in the environment.