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Mandarin fish (Siniperca chuatsi) is a valuable freshwater fish species widely cultured in China. Its aquaculture production is challenged by bacterial septicaemia, which is one of the most common bacterial diseases. Antimicrobial peptides (AMPs) play a critical role in the innate immune system of fish, exhibiting defensive and inhibitory effects against a wide range of pathogens. This study aimed to identify the antimicrobial peptide genes in mandarin fish using transcriptomes data obtained from 17 tissue in our laboratory. Through nucleotide sequence alignment and protein structural domain analysis, 15 antimicrobial peptide genes (moronecidin , pleurocidin , lysozyme g , thymosin β 12 , hepcidin , leap 2 , β-defensin , galectin 8 , galectin 9 , apoB , apoD , apoE , apoF , apoM , and nk-lysin) were identified, of which 9 antimicrobial peptide genes were identified for the first time. In addition, 15 AMPs were subjected to sequence characterization and protein structure analysis. After injection with Aeromonas hydrophila , the number of red blood cells, hemoglobin concentration, and platelet counts in mandarin fish showed a decreasing trend, indicating partial hemolysis. The expression change patterns of 15 AMP genes in the intestine after A. hydrophila infection were examined by using qRT-PCR. The results revealed, marked up-regulation (approximately 116.04) of the hepcidin gene, down-regulation of the piscidin family genes expression. Moreover, most AMP genes were responded in the early stages after A. hydrophila challenge. This study provides fundamental information for investigating the role of the different antimicrobial peptide genes in mandarin fish in defense against A. hydrophila infection. • 15 AMP genes were identified from the transcriptomes of Siniperca chuatsi , of which nine genes were firstly identified. • Most AMPs in the intestine of S. chuatsi were responded at the early stage (0–48 h) after challenged by A. hydrophila. • The expression of the hepcidin gene was the highest up-regulated in the intestine following infection with A. hydrophila. • The expression of the piscidin family genes were down-regulated in the intestine during A. hydrophila challenge. [ABSTRACT FROM AUTHOR]