Hibiscus sabdariffa extract (HSE) and Syzygium cumini extract (SCE) have been used in traditional medicine due to their hypoglycemic, antidiabetic, anti-obesity and antioxidant activities. This study aimed to evaluate the anti-obesity effects of these extracts, as well as to evaluate their toxicities. The phytochemical profiles were obtained by HPLC-DAD-ESI-MS/MS analyses. Pharmacological screening, motor activity, motor coordination and acute toxicity were evaluated by administering HSE or SCE (oral or intraperitoneal routes) at different doses to mice. The anti-obesity effects were examined by assessing the decrease in food intake and body weight loss in Wistar albino rats and by gastrointestinal transit in Swiss albino mice. Sibutramine was used as the positive control. Both extracts showed no toxic effects. At the end of 7 days of treatment, we observed that SCE and HSE reduced the weight gain and food intake of the treated rats in relation to the controls. Sub-chronic treatment revealed that HSE, SCE and sibutramine had the best effect 7 and 14 days after starting treatment. After 28 days, the SCE group showed less weight gain and reduced food consumption compared to the HSE group and controls. In addition, intestinal transit was increased in the HSE group, which is probably due to the high fiber content of the extract and may explain its anti-obesity properties. Myricetin glycosides were found in high levels in SCE and low levels in HSE, which may be the main compounds associated with the anti-obesity effect found in SCE. It is not possible to suggest an effective dose without conducting a preclinical toxicology study. We recommend clinical studies that evaluate the efficacy and safety, as well as the effect of discontinuing the extracts.