This study investigated the anti-obesity effects of fucoxanthin in diet-induced obesity mice fed a high-fat diet (20% fat, wt/wt). The mice were supplemented with two doses of fucoxanthin (0.05 and 0.2%, wt/wt) for 6 wk. Fucoxanthin significantly lowered body weight and visceral fat-pads weights compared with the control group without altering food intake. In epididymal adipose tissue of fucoxanthin-fed mice, adipocyte sizes and mRNA expression of lipogenic and fatty acid β-oxidation enzymes were significantly altered in a dose-dependent manner. Plasma leptin level was significantly lower in the fucoxanthin groups than in the control group, while the adiponectin level was elevated. Fucoxanthin significantly down-regulated various lipogenic enzyme activities in epididymal adipose tissue with a simultaneous decrease in fatty acid β-oxidation activity. The 0.2% fucoxanthin supplement led to increase mRNA expression of uncoupling protein-1 (UCP-1) and UCP-3 in brown adipose tissue and that of UCP-2 in the epididymal white adipose tissue. However, the 0.05% fucoxanthin only elevated UCP-1 mRNA expression in epididymal white adipose tissue. These results suggest that the anti-obesity effect of fucoxanthin could be mediated by altering lipid-regulating enzymes and UCPs in the visceral fat tissues and plasma adipokine levels.