The present work investigated the effect of NaCl and seawater salinity (SWS) on accumulation of proline and glycinebetaine (betaine) and expression of two key enzymes of their biosynthetic pathway, betainealdehyde dehydrogenase (BADH) and ”1-pyrroline-5-carboxylate synthetase (P5CS) in two aquatic macrophytes, salt-tolerant Najas gramenia and moderately-salt-tolerant Najas indica. N. gramenia did not show any accumulation of betaine or expression of BADH in response to NaCl or SWS treatments. The content of proline increased significantly in response to the salt treatments. High expression of P5CS was also observed, however, the transcript abundance did not correlate with the amount of proline. N. indica, exhibited significantly greater accumulation of proline in response to SWS, which contained Ca2+ in addition to NaCl, than in response to NaCl alone.