Altered levels of adipokines, derived as a result of distorted adipocytes, are the major factors responsible for changing biochemical parameters in obesity that leads to the development of metabolic disorders such as insulin resistance and atherosclerosis. In our previous reports, chitosan oligosaccharides (CO) were proved to inhibit the differentiation of 3T3-L1 adipocytes. In the present study, an attempt was made to investigate the anti-obesity and anti-diabetic effect of CO on ob/ob mice, by means of differential proteomic analysis of plasma. This was followed by immunoblotting, and gene expression in adipose tissue to clarify the molecular mechanism. CO treatment showed reduced diet intake (13%), body weight gain (12%), lipid (29%) and glucose levels (35%). 2-DE results showed differential levels of five proteins namely RBP4, apoE, and apoA-IV by >2-fold down-regulation and by >2-fold of apoA-I and glutathione peroxidase (GPx) up-regulation after CO treatment. Immunoblotting studies of adiponectin and resistin showed amelioration in their levels in plasma. Furthermore, the results of gene expressions for adipose tissue specific TNF-alpha, and IL-6 secretary molecules were also down-regulated by CO treatment. Gene expressions of PPAR gamma in adipose tissue were in good agreement with the ameliorated levels of adipokines, thereby improving the pathological state. Taken together, CO might act as a potent down-regulator of obesity-related gene expression in ob/ob mice that may normalize altered plasma proteins to overcome metabolic disorders of obesity.