CpG-oligodeoxynucleotides (CpG-ODNs) are potent immune stimuli currently under investigation as antimicrobial agents for different species. Toll-like receptor (TLR) 9 and TLR21 are the cellular receptors of CpG-ODN in mammals and chickens, respectively. The avian genomes lack TLR9, whereas mammalian genomes lack TLR21. Although fish contain both of these genes, the biological functions of fish TLR9 and TLR21 have not been investigated previously. In this study, we comparatively investigated zebrafish TLR9 (zebTLR9) and TLR21 (zebTLR21). The two TLRs have similar expression profiles in zebrafish. They are expressed during early development stages and are preferentially expressed in innate immune function-related organs in adult fish. Results from cell-based activation assays indicate that these two zebrafish TLRs are functional, responding to CpG-ODN but not to other TLR ligands. zebTLR9 broadly recognized CpG-ODN with different CpG motifs, but CpG-ODN with GACGTT or AACGTT had better activity to this TLR. In contrast, zebTLR21 responded preferentially to CpG-ODN with GTCGTT motifs. The distinctive ligand recognition profiles of these two TLRs were determined by their ectodomains. Activation of these two TLRs by CpG-ODN occurred inside the cells and was modulated by UNC93B1. The biological functions of these two TLRs were further investigated. The CpGODNs that activate both zebTLR9 and zebTLR21 were more potent than others that activate only zebTLR9 in the activation of cytokine productions and were more bactericidal in zebrafish. These results suggest that zebTLR9 and zebTLR21 cooperatively mediate the antimicrobial activities of CpG-ODN. Overall, this study provides a molecular basis for the activities of CpG-ODN in fish.pattern recognition receptor | innate immunity | adjuvant B acterial and viral CpG-deoxynucleotides containing DNA (CpG-DNA) represent a type of pathogen-associated molecular pattern (PAMP) that activates immune cells and triggers host responses to microbial infections (1-3). Synthetic phosphorothioate-modified CpG-oligodeoxynucleotides (CpG-ODNs) mimic the functions of CpG-DNA and have been investigated as immune modulators for their adjuvant and antimicrobial activities in different species (4-7). In general, a CpG-ODN contains one or more copies of CpG-deoxynucleotides containing hexamer motifs (CpG motifs). A CpG-ODN's immunostimulatory activities are dependent on its length, the number of CpG motifs, and the position, spacing, and surrounding bases of these CpG motifs.A CpG-ODN can have varying immunostimulatory activity in different species. This species-specific property is determined by the nucleotide context of the CpG motifs within the CpG-ODN. For example, CpG-ODNs containing a purine-purine-CGpyrimidine-pyrimidine motif, such as a GACGTT motif, are more potent in activating murine cells compared with those containing a GTCGTT motif. In contrast, the GTCGTT motif containing CpG-ODN generates stronger immune responses in humans and various domestic animals (8, 9).Toll-like receptors (...