Abstract: In this study, the phenylpropanoid pathway of the interaction of wolfberry and root rot pathogens will be discussed. The relationship between wolfberry phenylpropanoid pathway and disease resistance will be clarified. In this study, the experimental materials are cultivated varieties NingqiⅠ, NingqiⅡ; domestic wild species Lyciumchinense,L.barbarum; wild species of America L.brevipes,L.exsertum. The strong pathogenic Fusariumoxysporum isolated from the onset of wolfberry will be inoculation by root cutting method. And the anti-sense wolfbeey will be choose. This 2 kinds of wolfberry as materials to study the change of phenylalanine ammonia lyase, cinnamic acid hydroxylase, 4-hydroxylase p-coumaric acyl-coenzyme A ligase, phenolics and flavonoids in 20 days. The results show that the disease resistance of wild materials are strong than the cultivated material in 6 kinds of test materials which were inoculated with wolfberry root rot strong pathogen F.oxysporum. NingqiⅠis susceptible materials. The resistance to root rot disease of L.exsertum are strongest. The key enzymes of phenylpropanoid pathway like phenylalnine ammonialyase, trans-cinnamic acid-4-hydroxylase, 4-coumarate: coenzyme A ligase activity are significantly higher than Ningqi Ⅰ. Initially identified the phenylalnine ammonialyase, trans-cinnamic acid-4-hydroxylase, 4-coumarate: coenzyme A ligase activity and flavonoid content of phenylpropanoid pathway of test material resistance to root rot disease was positively correlated. Therefore, the phenylalnine ammonialyase, trans-cinnamic acid-4-hydroxylase, 4-coumarate: coenzyme A ligase enzyme activity and flavonoid content can be a screening of anti-Chinese wolfberry Fusarium root rot of biochemical indexes preliminary.