Pure lead molecules, showing anti-inflammatory effect were isolated from the marine Pseudomonas aeruginosa PS3 (GenBank Accession No. EF488968) and Pseudomonas fluorescens PS7 (GenBank Accession No. EF488969) using solvent extraction procedures, subsequent column fractionation, followed by bio activity based screening. The structures of the lead molecules (3S, 8aS)-3-isobutylhexahydropyrrolo[1,2-a]pyrazine-1,4-dione (Compound 1) and (8aS)-3-(4-hydroxybenyl) hexahydropyrrolo[1,2-a]pyrazine-1,4-dione (Compound 2) obtained from P. aeruginosa PS3 and P. fluorescens PS7 respectively were established employing spectral analysis. Compounds 1 and 2 at their IC(50) values of 84 and 53μM concentrations respectively down regulated expression of tumor necrosis factor-α (TNF-α) and interleukin 1-β (IL-1β) in peripheral blood mononuclear cells (PBMCs) and inducible nitric oxide synthase (iNOS) gene in RAW 264.7 cells. Immunoblot analysis revealed the inhibitory effect of pure compounds on phosphorylation of all the three mitogen activated protein kinases (MAPK) such as ERK, JNK and p38 MAPK. The results of the present investigation revealed that the pure compounds are anti-inflammatory in nature.