The full-length cDNA sequence of Toll-like receptor 9(CiTLR9)gene was identified from grass carp(Ctenopharyngodon idella)gill by homologous cloning and rapid amplification cDNA ends(RACE).The CiTLR9 cDNA was 3 468 bp,encoding 1 058 amino acid(aa)residues,including signal peptide,16 leucine rich repeat(LRR)motifs,one transmembrane zone and one Toll/IL-1 receptor(TIR)domain.The molecular weight of the deduced protein is 121 921 u,and the isoelectric point is 8.80.The amino acid sequence of CiTLR9 possessed 85%,82%,55%,and 55% identity with the TLR9s of Cyprinus carpio,Danio rerio,Salmo salar and Oncorhynchus mykiss respectively.CiTLR9 protein firstly clustered with TLR9s in Cyprinidae species,Cyprinus carpio and Danio rerio in the phylogenetic analysis.CiTLR9 mRNA was detected in all the tested 15 tissues(blood,brain,eye,foregut,midgut,hindgut,gas bladder,gill,head kidney,trunk kidney,heart,hepatopancreas,muscle,skin,spleen)by semi-quantitative real-time RT-PCR,highly in gill,blood and head kidney.The results serve further studies on functions of TLR9 and exploitation of immunostimulators in grass carp.