Abstract: γ-aminobutyric acid receptor (GABAR) mainly exist in the central nervous system of vertebrates and invertebrates (CNS), it is the important targets of pesticides such as fipronil, abamectin, endosulfan and lindane. In order to clarify the molecular mechanism of GABA antagonists pesticides effects on the fishes, and the affinity with pesticide molecules, bioinformatic methods were used to search GABAAR β3 gene sequences that had released in the NCBI genome databases and did homologous alignment. Degenerate primers were designed in the highly conservative district. The full length cDNA sequence of GABAAR β3 of Carassius auratus was cloned successfully by RT-PCR and RACE PCR technology. The gene is 2 767 bp (GenBank ID: KC964110), with an open reading frame (ORF) of 1 506 bp, encoding 502 amino acids. Multiple sequence alignment indicated that it was highly conserved with other known β3 subunits. QRT-PCR amplification was used to detect the activity of transcription of the gene in different tissues and organs of C. crassius. The results indicated that it was differentially expressed in organs of Carassius auratus.