The root cap cells of CB37 and NB37 were divided into 4 groups,in which 3 groups were induced by 50 μg/mL,100 μg/mL,150 μg/mL of Helminthosporium maydis C toxin(HMC toxin) as the experimental group, and one group induced by pH 6.5 PBS as the control group. The inducing time was 1 h, 4 h and 7 h. The apoptosis of root cap cell was examined with 3 methods: neutral red and Evans blue staining, AO and EB staining and Hoechst 33258 staining. In the process of induction with HMC toxin, apoptotic bodies appeared in root cap cells and the chromosome morphology became marginate. Living and death cells could be clearly detected after Neutral red and Evans blue staining and the ratio of death in CB37 cells treated with 150 μg/mL HMCtoxin was higher than that of NB37 with the maximum death rates of 99.2% and 95.5%. Living, necrosis and apoptosis cells could be distinguished clearly by AO and EB complex staining and Hoechst 33258 staining. The ratio of apoptosis in cells of CB37 was much higher than that of NB37, the max ratio of apoptosis cells of CB37 and NB37 were 70.2％ and 36.7％. In contrast, the max ratio of apoptosis cells of CB37 and NB37 were 74.5％ and 30.7％ stained by Hoechst 33258 respectively. The max ratio of apoptosis in CB37 and NB37 occurred in 150 μg/mL HMC toxin treated for 7 h. Therefore, a conclusion can be made as follows: during the process of the "harm" by HMC toxin, apoptosis appeared in the root cap cells, the ratio of apoptosis in C cytoplasm was higher than that in N cytoplasm. Along with the increase of the toxin concentration and treating time, the ratio of apoptosis became higher. In spite of the different staining methods by AO and EB or by Hoechst 33258, the ratio of the cell apoptosis was similar. But the early and late apoptotic cells can be distinguished only by AO and EB complex staining.