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Carbon dots (C-dots) are a promising class of carbonaceous nanomaterials for bioimaging, catalysis, and optoelectronics. However, their applications are disrupted by recent reports that bright molecular fluorophores are co-produced in the synthesis of C-dots, in particular ones prepared through a bottom-up approach (carbon nanodots (CNDs)), commonly derived from citric acid precursors. The presence of highly emissive molecular fluorophore species obscures the true performance of CNDs and severely challenges the development of CNDs. Here we observe that the issue of molecular fluorophore impurity is still problematic for CNDs which are derived from a different type of precursor, polycylic aromatic hydrocarbons (PAHs). In this study, low-oxygen-content CNDs and small molecular fluorophores are co-produced through hydrothermal condensation of nitropyrene. Extensive and systematic characterization following column chromatographic separation and solvent-induced extraction reveals that molecular fluorophores and CNDs are clearly dissimilar in structure and optical properties. This work highlights that rigorous separation and purification steps need to be taken not only for hydrophilic CNDs but also for low-oxygen-content CNDs.