This chapter highlights some recently published outstanding researches that have pushed further the boundary of photoluminescent carbon nanomaterials applications to biological systems and have brought invaluable insights into cellular and organism dynamics. From our perspective, there is a need for nanoparticle-based methodologies that allow researcher to access the spatiotemporal dynamics inherent to a wide variety of biological processes. Two carbon allotropes have recently shown remarkable advances in neurosciences: fluorescent nanodiamonds (FND) (1) and single wall carbon nanotube (SWCNT) (2). We highlight in this chapter three examples of recent archetypical achievements based on the tracking of FNDs or SWCNTs while being aware that we are not exhaustive. Single particle tracking of FND was used to monitor the endosomal transport inside hippocampal neurons dissociated from mouse embryos and the author used this nanoparticle-based technique to unravel transport defects in mouse models of brain diseases. Single particle tracking of SWCNT was used to study the nanoscale organization and rheological properties of the extracellular space in acute slices of mouse brain. Altogether, this chapter reviews a decade of research related to FND and SWCNT tracking in cells (such as cancer cell lines and neurons) and organisms (such as zebrafish, drosophila embryos, C-elegans and mice).