Because of the superiority of GQDs (graphene quantum dots) in biomedical imaging, in terms of biocompatibility and toxicity of semiconductor quantum dots, GQDs bring new opportunities for the diagnosis and detection of diseases. In this study, we synthesized photoluminescent (PL) graphene quantum dots (GQDs) through a simple exfoliation and oxidation process, and then coated them with polydopamine (pDA) for enhanced stability in water and low toxicity in vivo. From the results, the GQDs coated with pDA showed an excellent stability of PL intensity. It showed that the PL intensity of noncoated GQDs in PBS solution rapidly decreased with time, resulting in a 45% reduction of the PL intensity for 14 days of incubation in PBS solution. After coating with polydopamine, PL intensities of polydopamine-coated GQDs was maintained more stably for 14 days compared with uncoated GQDs. We have observed the in vitro and in vivo biocompatibility of pDA-coated GQDs in nude mice. The overall observation revealed that pDA-coated GQDs could be used as a long-term optical imaging agent as well as a biocompatible drug carrier.