Incorporating an organic fluorescence agent into nanoparticles can significantly promote its fluorescent efficiency. In this article, a novel fluorescein isothiocyanate labeling aminated agarose (FITC-AA) was synthesized and tested as an effective fluorescent labeling agent. FITC-AA could spontaneously form nanoparticles with a diameter less than 200 nm below 37°C due to gelling effect of the agarose. Cell culture experiments confirmed that 3T3 fibroblast cells could be marked by fluorescent FITC-AA nanoparticles and the labeling time sustained longer than by FITC alone. This finding demonstrates that the fluorescent labeling of cells can be enhanced when fluorescent nanoparticles are used as markers.