Graphene-based nanomaterials, due to their unique physicochemical properties, versatile surface functionalization, ultra-high surface area, and good biocompatibility, have attracted considerable interest in biomedical applications such as biosensors, drug delivery, bioimaging, theranostics, and so on. In this review, we will summarize the current advances in bioimaging of graphene-based nanomaterials, including graphene, graphene oxide (GO), reduced graphene oxide (rGO), graphene quantum dots (GQDs), and their derivatives. There are two methods to synthesize graphene-based nanomaterials: in situ synthesis and binding method. We will highlight the molecular imaging modalities including optical imaging (fluorescence (FL), two-photon FL, and Raman imaging), PET/SPECT (positron emission tomography/single photon emission computed tomography), MRI (magnetic resonance imaging), PAI (photoacoustic imaging), CT (computed tomography), and multimodal imaging. In the end, we will elaborate on the prospects and challenges of their future bioimaging applications.