Guanidinylated chitosan derivatives with different molecular weights have been synthesized by the guanidinylation reaction of chitosan with aminoiminomethanesulfonic acid (AIMSOA); the structures of AIMSOA and guanidinylated chitosan were characterized by UV, FT-IR, fluorescence and 13C NMR. The absorbance at 230 nm, a emission band ranging from 500 to 540 nm in emission spectrum were observed. In addition, the strong peaks at 1649, 1555, 1380 cm−1, the distinct signals at 158.3 ppm in 13C NMR were found. The substitution degrees of guanidinylated chitosan were confirmed by elemental analysis. In vitro antibacterial activity of guanidinium derivatives was evaluated against Staphylococcus aureus, Bacillus subtilis, Escherichia coli and Pseudomonas aeruginosa. Compared with chitosan, guanidinylated chitosan had much better antibacterial activity, whose minimum inhibitory concentrations in aqueous hydrochloric acid (pH 5.4) were 4 times lower than those of chitosan. Interestingly, guanidinylated chitosan inhibited the growth of S. aureus and B. subtilis at pH 6.6. The antibacterial activity of guanidinylated chitosan enhanced with decreasing pH.