Innate immune system plays a significant role in all multicellular organisms and the key feature of the system is its ability to recognize and respond to invading microorganisms. Vertebrates including teleost fish have evolved an array of germ-line encoded pathogen recognition receptors (PRRs) for detecting and responding to various pathogens associated molecular patterns (PAMPs). Among the PRRs, Toll-like receptors (TLRs) that recognize the ligands on either extracellular surface or within the endosome, and two cytosolic receptors, nucleotide-binding domain, leucine-rich repeat containing receptors (NLRs) and retinoic acid inducible gene I (RIG-I)-like receptors (RLRs) are the three major classes. We identified twenty members of NLR gene family, three RLRs and seventeen TLRs from catfish RNA-seq and genome database. The identified NLRs included five already reported members of NODs (NLR-A subfamily) with a new NOD3a protein, two members of NLR-B subfamily, eleven genes of NLR-C subfamily many of which showed C-terminal B30.2 domain, apart from CIITA (NACHT-LRR), Apaf1 (CARD-NB/ARC-WD40) and NACHT-P1 (AAA-WD40). Retinoic acid inducible gene protein (RIG-I), melanoma differentiation-associated gene 5 (MAD5) and laboratory of genetics and physiology 2 (LGP2) constituted the RLRs. The identified TLRs included ((TLR1-4, TLR5m and TLR5s, TLR7, TLR8a and 8b, TLR18a and 18b, TLR19, TLR20a, 20b, TLR21 and TLR22). Expression of representative genes from different NLR subfamily and other members, all the three RLR and TLR genes were confirmed by reverse-transcriptase (RT)-PCR in eleven tissues of catfish. Majority of the genes were found to be ubiquitously expressed in all the tissues tested. Using quantitative real-time PCR, modulation in mRNA expression of selected NLR and TLR genes was elucidated in different tissues collected at four time points after bacterial infection with Edwardsiella ictaluri, the causative agent of enteric septicemia of catfish. The induction of some of the NLR and TLR genes observed in the infected fish indicated their involvement in catfish immunity against intracellular pathogens. This is the first comprehensive report of pathogen recognitions receptor repertoire in channel catfish.