Fluorescent nanodiamonds (FNDs) with a size in the range of 10 – 100 nm have been produced by ion irradiation and annealing, and isolated by differential centrifugation. Single particle spectroscopic characterization with confocal fluorescence microscopy and fluorescence correlation spectroscopy indicates that they are photostable and useful as an alternative to far-red fluorescent proteins for bioimaging applications. We demonstrate the application by performing in vivo imaging of bare and bioconjugated FND particles (100 nm in diameter) in C. elegans and zebrafishes and exploring the interactions between this novel nanomaterial and the model organisms. Our results indicate that FNDs can be delivered to the embryos of both organisms by microinjection and eventually into the hatched larvae in the next generation. No deleterious effects have been observed for the carbon-based nanoparticles in vivo. The high fluorescence brightness, excellent photostability, and nontoxic nature of the nanomaterial have allowed long-term imaging and tracking of embryogenesis in the organisms.