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Sea cucumber body wall contains several naturally occurring bioactive components that possess health-promoting properties. <i>Isostichopus badionotus</i> from Yucatan, Mexico is heavily fished, but little is known about its bioactive constituents. We previously established that <i>I. badionotus</i> meal had potent anti-inflammatory properties in vivo. We have now screened some of its constituents for anti-inflammatory activity in vitro. Glycosaminoglycan and soluble protein preparations reduced 12-O-tetradecanoylphorbol-13-acetate (TPA)-induced inflammatory responses in HaCaT cells while an ethanol extract had a limited effect. The primary glycosaminoglycan (fucosylated chondroitin sulfate; FCS) was purified and tested for anti-inflammatory activity in vivo. FCS modulated the expression of critical genes, including NF-ĸB, TNFα, iNOS, and COX-2, and attenuated inflammation and tissue damage caused by TPA in a mouse ear inflammation model. It also mitigated colonic colitis caused in mice by dextran sodium sulfate. FCS from <i>I. badionotus</i> of the Yucatan Peninsula thus had strong anti-inflammatory properties in vivo.