Abstract: To clarify the key differentiation stage of the root endogenous phytohormones and physiological indices between perennial buckwheat and annual buckwheat, three endogenous phytohormones（IAA, CTK and GA） and seven physiological indices（SOD, CAT, POD, GPX, GR, GST and APX） were compared during different developmental stages of root. The results showed that the endogenous phytohormones and enzymatic activities exhibited different trends during root development. The key differentiation stage between perennial buckwheat and annual buckwheat was the first flowering stage. This stage was the turning point for the five indices, namely GA, IAA, POD,GST and APX. Pearson correlation analysis showed that there were definite correlations among 10 indices, which could be divided into three categories. The first category included three indexes（IAA, GA and GR）. The second category included five indices（CAT, CTK, POD, GST and APX）. The third category included two indices（SOD and GPX）.