According to the study on the agronomic characteristics such as plant height,technical length,fiber percentage,the content of MDA and activity of POD between different varieties of flax in waterlogging stress,the physiological mechanisms of resistance to waterlogging of flax was opened out primarily.The results indicated that: 1.Waterlogging stressing has effects on economic characters of flax.The plant height,technical length,fiber percentage of flax are decreased.Aerenchyma in root is an important characteristic for measuring the tolerance of waterlogging;2.With the increasing time of stressing of waterlogging,the content of MDA increased,and the variation of the intolerant variety is more remarkable,so it shows that the tolerant variety has highly efficiency on resisting overoxidation of epicyte;3.With the increasing time of stressing of waterlogging,the activity of POD increased at first,and decreased as followed.The variation of the tolerant variety is more obvious.It shows that the tolerant variety is more efficient in eliminating active oxygen.