Rapid and recent progress in fluorescence microscopic techniques has allowed for routine discovery and viewing of biological structures and processes in unprecedented spatiotemporal resolution. In these imaging techniques, fluorescent nanoparticles (NPs) play important roles in the improvement of reporting systems. A short overview of recently developed fluorescent NPs used for advanced in vivo imaging will be discussed in this mini-review. The discussion begins with the contribution of fluorescence imaging in exploring the fate of NPs in biological systems. NP applications for in vivo imaging, including cell labeling, multimodal imaging and theranostic agents, are then discussed. Finally, despite all of the advancements in bioimaging, some unsolved challenges will be briefly discussed concerning future research directions.