Melilotus species (Fabaceae) have provided extensive anti-inflammatory traditional uses, and thus, they will continue to be among the major plant sources of possibly new anti-inflammatory drugs. In continuation of our previous chemical and biological studies on Melilotus indicus (L.) and Melilotus messanensis (L.)., the present work constructs a comparative anti-inflammatory evaluation of both plants and highlights their bioactive potential concerning their chemical components. The phenolic and flavonoid contents of the aqueous methanol extract (AME) of both plants were estimated spectrophotometrically and calculated to be (24.522 and 29.696 mg Gallic/g extract) and (7.429 and 11.344 mg Catechin/g extract) in (M. indicus and M. messanensis), respectively. Chronic toxicity tests of AME for each species were investigated after long-term daily oral administration (100 mg/kg B.wt.) to the experimental animals, where no significant change in their body and visceral organ weights. Also, the level of some biochemical markers like creatinine, urea, glucose, triglycerides, cholesterol, AST, and ALT was measured in the animal blood sera and found that there are no fluctuations occurred to their typical levels, therefore, both plants were mostly safe. Furthermore, AME, petroleum ether extract (PEE), and defatted AME (DAME) of M. indicus and M. messanensis were subjected to anti-inflammatory assay using carrageenan-induce paw edema models and exhibited significant potentials through inhibition of the rat paw edema diameter (13 and 12%), (11 and 10%), and (14 and 15%) for M. indicus and M. messanensis, respectively, in comparison with indomethacin (6%).