Chitosan biguanidine hydrochloride was synthesized by reacting chitosan with dicyandiamide under microwave irradiation. The influence of reaction temperature, reaction solvent and microwave heating time was studied, and optimal conditions were identified. The representative microwave synthesized chitosan biguanidine hydrochloride was characterized by Fourier transform infrared spectroscopy, scanning electron microscopy and X-ray diffraction measurement, taking chitosan as a reference. The solubility pH for the chitosan biguanidine hydrochloride with different substitution degrees was monitored. The antimicrobial activities of chitosan biguanidine hydrochloride were measured by means of the minimal inhibition concentration (MIC). In vitro antimicrobial activity of guanidinylated chitosans with different substitution degrees were evaluated against staphylococcus aureus, bacillus subtilis, escherichia coli and pseudomonas aeruginosa. The results show that the microwave irradiation method can increase the reaction rate by twelve times over the conventional method. Chitosan biguanidine hydrochloride are effective of bacteriostasis, compared with chitosan, guanidinylated chitosan had much better antibacterial activity. The antibacterial activity of chitosan biguanidine hydrochloride derivative enhanced with increasing substitution degrees of guanidinylated chitosan.