Fluorescent nanodiamonds are biocompatible fluorescent particles with indefinite photo-stability that make them superior in vitro and in vivo imaging probes for a wide range of applications. Fluorescence arises from specific defect centers within the nanodiamond lattice, which permits the generation of fluorescent nanodiamonds with different emission wavelengths, or combinations of emission wavelengths. The negatively charged nitrogen-vacancy (NV-) center is a defect in the diamond lattice consisting of a substitutional nitrogen and a lattice vacancy that form a nearest-neighbor pair. NV- centers are fluorescent sources with remarkable optical properties including quantum efficiency near unity, indefinite photo-stability, i.e., no photo-bleaching or blinking, broad excitation spectra, and sensitive magnetic field-dependent fluorescence emission. In particular, their near infrared fluorescence makes them well-suited for in vivo imaging. However, producing, functionalizing, and characterizing small bright FNDs for biomedical applications remains challenging. We have developed multiple biocompatible functionalization schemes that permit the stabilization and specific labeling of fluorescent nanodiamonds for biological imaging applications. I will describe an approach to significantly increase the density of carboxylic acid groups on the surface of nanodiamonds and demonstrate subsequent functionalization of the nanodiamonds via carboxylic acid coupling schemes. I will also describe a complementary encapsulation approach in which nanodiamonds are coated with a conformal layer of polydopamine, which is subsequently covalently functionalized. I will illustrate uses of FNDs for high resolution three dimensional single-molecule imaging, in vivo background-free imaging through magnetic modulation of FND emission, and as superior fiducial markers for super-resolution microscopies.