To investigate whether toll like receptors (TLRs) genes do have an immune influence on noble scallop Chlamys nobilis under pathogen stress, acute challenges lasting 48 h to Vibrio parahaemolyticus, lipopolysaccharide (LPS), polyinosinic polycytidylic acid (Poly I:C), and PBS were conducted in two scallop stains of orange and brown with different carotenoids content. A novel toll-like receptor gene called CnTLR-1 was cloned and its transcripts under different challenges were determined. Meantime, total carotenoids content (TCC) of different immune responses were determined to investigate whether there was a relationship between gene expression and carotenoids content. The full length cDNA of CnTLR-1 is 2982 bp with an open reading frame (ORF) of 1920 bp encoding 639-deduced amino acids, which contains five leucine-rich repeats (LRR), two LRR-C-terminal (LRRCT) motifs and a LRR-N-terminal (LRRNT) motif in the extracellular domain, a transmembrane domain and a Toll/Interleukin-1 Receptor (TIR) of 138-amino acids in the cytoplasmic region. Phylogenetic tree analysis showed that CnTLR-1 could be clustered with mollusk TLRs into one group and especially was related closely to Crassostrea gigas and Mytilus galloprovincialis TLRs. CnTLR-1 transcripts were detected in decreasing levels in the mantle, hemocytes, gill, kidney, gonad, hepatopancreas, intestines and adductor. Compared with PBS control group, CnTLR-1 transcripts were up-regulated in V. parahaemolyticus, LPS and Poly I:C groups. Further, CnTLR-1 transcripts were significantly higher in orange scallops than that of brown ones with and without pathogenic challenges. TCC, which is higher in orange scallops, was initially increased and then decreased during a 48 h immune challenge in the hemocytes. The present results indicate that CnTLR-1 is an important factor involved in the immune defense against pathogens in the noble scallop.