Bioimaging, serving as one of the most important techniques, provides direct visualization of biological systems. Biological probes are essential tools for bioimaging applications. Scientists have devoted tremendous efforts to developing various kinds of fluorescent nanomaterials (e.g., II-VI semiconductor quantum dots, fluorescent carbon nanodots, fluorescent nanodiamonds, silicon nanoparticles (SiNPs))-based bioprobes, significantly facilitating the advancement of bioimaging applications. Among them, SiNPs are regarded as potentially ideal fluorescent bioprobes due to their unique optical properties (e.g., high fluorescence and strong antiphotobleaching property) and excellent biocompatibility. In the past decade, SiNPs-based fluorescent bioprobes have been extensively explored for in vitro and in vivo imaging. Of particular significance, taking advantage of their ultrahigh photostability and non or lowly toxic properties, fluorescent SiNPs-based nanoprobes are demonstrated to be superbly suited to long-term and real-time bioimaging applications. Also of note, multifunctional SiNPs with fluorescent and magnetic properties have been developed for multimodel bioimaging studies in recent years.