Expression analysis of crop plants has improved our knowledge about the veiled underlying mechanisms for salt tolerance. In order to observe the time course effects of salinity stress on gene expression for enzymes regulating proline metabolism, we comparatively analyzed the expression of specific genes for proline metabolism in root and shoot tissues of salt-tolerant (cv. Dunkled) and salt-sensitive (cv. Cyclone) canola (Brassica napus L.) cultivars through reverse-transcriptase polymerase chain reaction (RT-PCR); following the NaCl treatment for various durations. Both lines showed an increase in ∆¹-pyrroline-5-carboxylate synthase1 (P5CS1) gene expression after induction of salt stress with enhanced expression in the root tissue of the tolerant line, while maximum expression was noted in the shoot tissues of the sensitive line. We observed a much reduced proline dehydrogenase (PDH) expression in both the root and shoot tissues of both canola lines, with more marked reduction of PDH expression in the shoot tissues than that in the root ones. To confirm the increase in P5CS1 gene expression, total proline content was also measured in the root and shoot tissues of both the canola lines. The root tissues of canola sensitive line showed a gradually increasing proline concentration pattern with regular increase in salinity treatment, while an increase in proline concentration in the tolerant line was noted at 24 h post salinity treatment after a sudden decrease at 6 h and 12 h of salt treatment. A gradually increasing concentration of free proline content was found in shoot tissues of the tolerant canola line though a remarkable increase in proline concentration was noted in the sensitive canola line at 24 h post salinity treatment, indicating the initiation of proline biosynthesis process in that tissue of sensitive canola.