The unique features of Mesoporous Silica Nanoparticles (MSNs) provide a suitable platform to carry fluorescence dyes for various bioimaging applications. Several strategies have been developed to conjugate a variety of dyes either in the pores or on the surfaces of MSNs to form the fluorescence MSNs (FMSNs). In this chapter, we will discuss recent research progress and future development of FMSNs for living system imaging. We will first describe different strategies for the fabrications of FMSNs. Then, we will discuss the recent developments of cellular and intracellular imaging including self-probe for the interactions of FMSNs with the cells, receptor and organelle labeling, sensing and tracking of biological system, and monitoring the drug delivery and release processes. Moreover, we will include the applications of FMSNs as contrast agents for in vivo imaging. Finally, we will conclude and highlight the challenges and opportunities for MSNs in medical applications.