Scavenger receptor class A member 5 (SCARA5) and high-mobility group box 1 (HMGB1) protein have become increasingly attractive for their critical functions in innate inflammatory reactions and disorders. However, the functional relevance between these two molecules has never been described. This study discovered that SCARA5 is an HMGB1 recognition receptor that is negatively involved in HMGB1-mediated inflammation in pufferfish (Tetraodon nigroviridis) and zebrafish (Danio rerio) models. Hence, SCARA5 is added as a new member to the HMGB1 receptor family. Tetraodon HMGB1 (TnHMGB1) is a trafficking protein that can be secreted from the nucleus to the outside of cells upon CpG-oligodeoxynucleotide (ODN) stimulation. This protein exerts a strong synergistic effect on CpG-ODN–induced inflammation, as determined by the enhanced proinflammatory cytokine expression through coadministration of TnHMGB1 with CpG-ODN and impaired inflammatory responses through TnHMGB1 depletion. Tetraodon SCARA5 (TnSCARA5) is an inducible protein detected upon TnHMGB1 stimulation; this protein plays an inhibitory role in CpG-ODN–induced inflammation because TnSCARA5 overexpression suppresses cell responsiveness to CpG-ODN induction, whereas TnSCARA5 ablation intensifies the inflammatory reactions. TnSCARA5 can strongly associate with TnHMGB1 through the A and B boxes, depending on the redox state of the cysteine residues, but T box inhibits the association. TnSCARA5 mediates the endocytosis of TnHMGB1 into lysosomes. Results suggest that TnSCARA5 inhibits the CpG-ODN–mediated inflammation via the clearance of HMGB1 mediator for CpG-ODN stimulant. The above findings highlight a novel regulatory mechanism underlying innate inflammation and provide new insights into the clinical treatment of HMGB1-mediated diseases.