Two soybean cultivars, one conventional and a glyphosate-tolerant (transgenic), were submitted to the water stress and the chlorophyll a fluorescence induced by UV light was monitored daily during 16 days. In this work, 40 pots in total, 20 per cultivar were used in the investigation. Each cultivar was divided in two groups, the control group and the group submitted to the water stress. The stress response of the cultivars was monitored by red to far-red fluorescence ratio. The data indicate that the water stress induced the earliest changes on the fluorescence ratio and chlorophyll content for the conventional cultivar. In addition, a comparative analysis of the fluorescence ratios of the cultivars reveals that conventional plants have higher chlorophyll content than transgenic ones. This result might be useful in the development of methodologies able to distinguish conventional to transgenic apart.