Carbonic anhydrase (CA) was identified by differential display PCR analysis as one of the differentially expressed genes in the gills of low salinity stressed (transferred from 25 to 3 ppt) Penaeusmonodon. To further characterize the role of CA in the regulation of salinity stress, the cDNA sequence of P.monodon carbonic anhydrase (PmCA) was attained by rapid amplification of cDNA ends and found to have a total length of 1194 bp. The deduced amino acid of PmCA shares 73% sequence identity with the CA homologue recently isolated from the crab, Callinectessapidus. Real time RT-PCR and enzymatic activity analyses were employed to determine the changes in the PmCA mRNA expression and total CA activity, respectively, after shrimps were transferred from 25 to 3 ppt salinities for up to 2 weeks. Compared to the CA level in the control group (25 ppt), PmCA mRNA was significantly increased in shrimp gills at 24 h after hypo-osmotic stress. In contrast, the epipodites and antennal gland displayed decreased levels of mRNA expression. The gross CA enzymatic activity after hypo-osmotic stress was increased in the shrimp gills but remained stable in the epipodites and antennal gland.