Phytochemical investigation of the roots of Echiochilon fruticosum resulted in the isolation of two naphthoquinone derivatives. Compound 1 was identified as anhydroalkanin while compound 2 was identified as a new derivative 5-hydroxy 8-methoxy 2-(4-methylpent-1,3-dienyl) naphthalene-1,4-dione named as echiochiloquinone. In addition, caffeic acid 3, caffeic acid methyl ester 4 were isolated. The structures were determined by physical, chemical and spectral methods. The anti-inflammatory activity of the root extracts and compound 2 was evaluated utilizing both cotton pellet-induced and carragenin-induced rat paw edema. The ulcerogenic effect was also studied.