Adipose tissue plays a central role in the development of obesity, and thus characterization of the molecular changes related to obesity in this tissue is a main concern. Recently we identified chitosan oligosaccharides (CO) as a potent adipogenic inhibitor in 3T3-L1 cells. In the current study, a proteomic approach was used to investigate the anti-obesity effect of CO in white adipose tissue of ob/ob mice. CO administration significantly lowered body weight gain and epididymal WAT mass compared to control animals. In addition, twenty-five proteins were found to be differentially expressed between the two groups of animals in response to CO treatment. Expression changes in Karyopherin beta 1, indoleamine-pyrrole 2,3-dioxygenase, and retinoic acid binding protein were associated here for the first time with obesity. Immunoblotting studies of adipocyte protein 2 (aP2) and aquaporin-7 also showed amelioration in their levels in WAT. Furthermore, the results of adipose tissue specific gene expressions of aP2, adiponectin, TNF-${alpha}$, and IL-6 were in good agreement with improved levels of obesity. Gene expression of PPARg and SREBP-1c were also down-regulated by CO treatment. The results suggest that the anti-obesity effect of CO might be mediated by the modulation of adipokines and adipose tissue specific genes.