Cotton-source cellulose nanocrystals (CNCs) with a range of surface charge densities were fluorescently labeled with 5-(4, 6-dichlorotriazinyl) aminofluorescein (DTAF) in a facile, one-pot reaction under alkaline conditions. Three CNC samples were labeled: (I) anionic CNCs prepared by sulfuric acid hydrolysis with a sulfur content of 0.47 wt %, (II) a partially desulfated, sulfuric acid-hydrolyzed CNC sample, which was less anionic with an intermediate sulfur content of 0.21 wt %, and (III) uncharged CNCs prepared by HCl hydrolysis. The DTAF-labeled CNCs were characterized by dynamic light scattering, atomic force microscopy, fluorescence spectroscopy and microscopy, and polarized light microscopy. Fluorescent CNCs exhibited similar colloidal stability to the starting CNCs, with the exception of the HCl-hydrolyzed sample, which became less agglomerated after the labeling reaction. The degree of labeling depended on the sulfur content of the CNCs, indicating that the presence of sulfate half-ester groups on the CNC surfaces hindered labeling. The labeling reaction produced CNCs that had detectable fluorescence, without compromising the overall surface chemistry or behavior of the materials, an aspect relevant to studies that require a fluorescent cellulose substrate with intact native properties. The DTAF-labeled CNCs were proposed as optical markers for the dispersion quality of CNC-loaded polymer composites. Electrospun polyvinyl alcohol fibers loaded with DTAF-labeled CNCs appeared uniformly fluorescent by fluorescence microscopy, suggesting that the nanoparticles were well dispersed within the polymer matrix.