Abstract: To investigate the effect of low salinity stress on Glucose-6-Phosphate Isomerase (GPI) in Takifugu rubripes, we cloned GPI and analyzed its expressions in tissues with and without acute low-salinity stress using RT-PCR and real-time quantitative PCR (qPCR) techniques. The results showed that the GPI cDNA of the T. rubripes was 1736 bp in length containing an Open Reading Frame of 1662 nucleotides that encodes 553 amino acids. The predicted amino acid sequence contains two Sugar Isomerase Domains without signal peptide and transmembrane domains. Results of multiple sequence alignment showed that GPI was highly conserved among species. qPCR results showed that GPI mRNA was expressed in all the tested tissues, with the highest expression level in muscle. Under low-salinity stress, the relative mRNA expression of GPI in gill increased firstly, then decreased and increased again in all low-salinity groups, and the relative mRNA expression of GPI in kidney differed among low-salinity groups. Therefore, it was speculated that GPI play a role in the response of T. rubripes to acute low-salinity stress.