Biocompatible glutaraldehyde-cross-linked chitosan with new red fluorescence were prepared for the first time and were shaped into nanoparticles via inverse-microemulsion method. They could luminesce at ca. 670 nm either as powders and nanoparticles or in real and gelling solutions or suspensions, having a lifetime of 1.353 ns and a quantum yield of 0.08 in solution or 0.01 in solid state. The new-formed pyridinium structures and the intramolecular charge transfer effect are considered to be responsible for the new red emission, which have been proved by FTIR, (13)C NMR, and some calculation using Gaussian 09, respectively. Strikingly, they are quite inert and anti-photobleaching, with only <3% loss of fluorescent intensity per minute in average under a continuous laser illumination at 633 nm and 50 μW. Especially, their nanoparticles (5.6 nm) could enter into the negative nucleoli of living HeLa cells with low cytotoxicity for high contrast imaging inspections.