Abstract: Carnitine palmitoyltransferase（CPT） is a key factor regulating the β-oxidation of long-chain fatty acids in vertebrates, including carnitine palmitoyltransferase 1（CPT1） and carnitine palmitoyltransferase 2（CPT2）, which plays an important role in energy metabolism. So far, many studies have provided evidence of a variety of CPT genes in bony fish, but the study of CPT gene in swamp eel（Monopterus albus） has not been reported. In this study, using the liver cDNA of swamp eel as a template, the open reading frame（ORF） sequences of CPT1A, CPT1B and CPT2 genes were obtained by nested PCR and TA cloning technique. The structural characteristics of the three genes were analyzed by bioinformatics software, and their expression in different tissues was detected by real time quantitative PCR. The results showed that the ORF sequences of CPT1A, CPT1B and CPT2 genes were 2 367, 2 361, and 2 004 bp, encoding 788, 786, and 667 amino acids, respectively, and the molecular weights of predicted mature peptides were 89.83, 89.70, and 74.55 kDa, respectively, and the secondary structures of the genes were mainly composed of α helix. Homology analysis showed that the CPT1A, CPT1B, and CPT2 protein of swamp eel had high homology with CPT proteins of the other species, all of which were more than 60%. The phylogenetic tree showed that the CPT1A, CPT1B, and CPT2 proteins of swamp eel were closely related to that of the spinous fin order of teleost. Tissue distribution analysis showed that the expression of CPT1A and CPT1B of swamp eel was the highest in heart, and the expression of CPT2 in stomach was the highest. By studying the expression and distribution of CPT1A, CPT1B, and CPT2 genes in swamp eel, we can infer that they may play a role in nutritional metabolism and gonadal development of swamp eel.