In this paper, two microalgal strains (Isochrysis galbana 3011 and 8701) were used to study the difference of chlorophyll a fluorescence parameters under high temperature stress (35-50 ℃). The results showed that the maximal photochemical efficiency of PSⅡ(F_v/F_m), the potential activity of PSII (F_v/F_o), the relative electron transport rate (rETR), the actual photochemical efficiency of the PSII reaction centers of light adapted cells (ΦPSII) and the photochemical quenching (qP) all decreased under high temperature stress in the two microalgal strains. The changed degree of the above parameters increased with the increase of temperature and the increasing exposure time. NPQ in the two microalgal strains exhibited different patterns of variation with high temperature stress, the values in 3011 first increased then decreased, while that in 8701 increased with stress time at 35 ℃and 40 ℃, but first increased then decreased at 45 ℃. There are some heattolerance varieties between the two microalgal strains 3011 and 8701. For 3011, the parameters F_v/F_m, F_v/F_o, ΦPSII, rETR and qP could almost recover to the control values in the normal temperature after 10 min high temperature treatments at 40 ℃, but could not recover when the stress temperature are at 45 ℃ and 50 ℃. As to 8701, the parameters F_v/F_m and F_v/F_o could almost recover to the control values at 25 ℃ after 10 min high temperature stress at 35 ℃ and 40 ℃, but all parameters could not recover to the control values when the temperature is above 45 ℃. The responsive mechanism of Isochrysis galbana to high temperature stress as well as the possibility of determining the high temperature resistance in microalgae using chlorophyl fluorescence induction kinetics was also discussed in this paper.