Aminopeptidase N is a member of the peptidase M1 family, and plays an important role in the digestion of protein. In this study, a full-length cDNA of APN gene was cloned from Ctenopharyngodon idellus with RT-PCR and RACE techniques, and its mRNA expression profile at different tissues was analyzed by real-time PCR method. The full-length of cDNA sequence of APN had 3 258 nucleotides, including 27 nucleotides at 5’UTR and 552 nucleotides at 3’UTR. Its open reading frame(ORF) had 2 679 nucleotides encoding a 892-amino-acid peptide. The deduced amino acid sequences of APN gene from C. idellus displayed the highest similarity with Danio rerio (75.4%), but varied to other animals from 61.2% to 58.8%. The encoded protein molecular weight was predicted at 100.61 ku with pI at 5.14. Phylogenetic analysis showed that the sequence of APN gene was clustered with D. rerio as its closest neighbor, which shared a sequence similarity of 81.5%, and had lower similarity with other animals from 60.2% to 54.3%. The APN protein had one helix trans-membrane region, but its amino acid sequence of the region demonstrated a low homology relationship to other vertebrates. The abundances of APN mRNA assayed by real-time PCR were differentially expressed at different tissues with a gradient from higher to lower among the tissues of fore-intestine, hind-intestine, liver, mid-intestine, kidney, muscle, spleen and heart, respectively. However, the APN mRNA expression was relatively stable after incubation for 4 days. The effects of the circadian rhythms on APN expression of C. idellus showed that there was a time-dependent pattern at higher rhythm during 06:00-18:00 and lower rhythm during 18:00-06:00. Therefore, our study could serve as an important research tool to study the relationship between APN gene’s function and its structure, and investigate its molecular mechanism for protein degradation in vivo.