The major products of chitosan degraded by chemical or enzymes are low molecular weight chitosan (low Mw chitosan) and chitooligosaccharide. In this thesis we utilized capillary zone electrophoresis (CZE) and capillary gel electrophoresis (CGE) to analyze the degree of deacetylation (DDA) and the molecular weight of the low Mw weight chitosan product. Furthermore, the composition analysis of chitooligosaccharide product was performed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry(MALDI-TOF/MS), and the averaged DDA was calculated based on the relative signals of chitooligosaccharides from mass spectra. Our CE and MALDI-TOF/MS methods feature fast measurement, high throughput, and microanalysis, and thus are advantageous to the time course study of various degradation reactions of chitosan from the one pot reaction. The DDA’s of low Mw chitosan and chitooligosaccharide produced from chitosan degradation by sodium persulfate (NaPS) are close to the DDA of the original chitosan sample (DDA85%). However, low Mw chitosan with DDA90% and chitooligosaccharide with DDA58% were obtained if pepsin was used to digest the same chitosan for 72 hours. Analyzing the compositions of the chitooligosaccharide products for both reactions after 3-hour degradation by MALDI-TOF/MS, we found that the major products obtained from pepsin digestion are chitooligosaccharides with low DDA’s. On the other hand, the NaPS degradation products are mainly chitooligosaccharides with high DDA’s. According to the results we infer that enzyme can selectively hydrolyze chitosan polymer chains on the low DDA regions, but NaPS seems to homogeneously fragment the polymer chains regardless of the monomer compositions. In order to study the effects of sample DDA on the aforementioned conclusion, we carried out different degrees of acetylation reactions to convert the DDA85% sample into two chitosan samples with similar molecular weight but different DDA’s at 55% and 33%, respectively. The three chitosan samples were then separately subjected to degradation reactions with NaPS and enzymes such as pepsin, lipase A, cellulase, bromelain, and papain. The experimental results revealed that the DDA’s of the low Mw chitosan and chitooligosaccharide produced by the NaPS degradation are the same as the original chitosan samples, while the DDA’s of the enzymatic digestion products are influenced by the type of enzymes as well as the DDA’s of the chitosan substrates. Additionally, we also investigated the differences in acetylation reactivity of fully deacetylated chitooligosaccharide (DDA100%) sample under acidic, neutral, and basic reaction conditions, and consequently obtained the optimal acetylation conditions to generate the fully acetylated chitooligosaccharide (DDA0%) sample. When analyzing the two chitooligosaccharide samples with the same concentration by MALD-TOF/MS, we found that the DDA0% samples are 4 to 6 times the MS signals of the DDA100% samples.