Polymeric immunoglobulin receptor (pIgR) is an important member of the immunoglobulin superfamily. It can mediate polarity transportation of polymeric immunoglobulin in mucosal epithelial cells and play an important role in innate and acquired immunity. In this study, the full‐length cDNA sequence of Carassius auratus indigentiaus pIgR gene was firstly cloned and characterized. The complete cDNA sequence of C. auratus indigentiaus pIgR gene is 1399 bp, including a 984 bp open reading frame that encodes 327 amino acids. The pIgR is composed of extracellular, transmembrane and intracellular regions, which are composed of 255, 23 and 49 amino acids, respectively. The extracellular region contains two Ig‐like domains (ILDs), ILD1 consists of 104 amino acids (25–128) and ILD2 consists of 93 amino acids (137–229). The similarity between the pIgR sequences of C. auratus indigentiaus and other fish is 65.95%–97.55%. Analysis of phylogenetic trees shows that pIgR of C. auratus indigentiaus clusters into one branch with the pIgR of Cypriniformes. QRT‐PCR analysis revealed that the pIgR gene expression was highest in liver, followed by intestine, gill, head kidney and skin. After challenge with Aeromonas hydrophila, the relative expressions of pIgR in different tissues first increased and then decreased within 96 h. Moreover, the expression of pIgR gene peaked earlier in mucosal immune tissues (intestines, gill and skin) than in system immune tissues. It suggested that pIgR might play an important role in mucosa‐associated lymphoid tissue to protect the C. auratus indigentiaus against Aeromonas hydrophila infection. [ABSTRACT FROM AUTHOR]