In this study, we investigated changes of fluorescence parameters, specific growth rate, and relative chlorophyll content (the ratio of the chlorophyll content after salinity exposure to that of the same samples at inoculation) in the two diatoms Phaeodactylum tricornutum Bohlin and Chaetoceros gracilis Schuett, during exposure of the cultures to different salinities (1–90 psu for P. tricornutum and 1–70 psu for C. gracilis ) for different times (12, 24, and 48 h). The results indicated that the maximal photochemical efficiency of PSII (F v /F m ), maximal relative electron transport rate (rETR max ), and photochemical quenching (qP) decreased significantly with the degree of salinity stress and increased with increasing exposure times in the two diatoms. For P . tricornutum , the values of F v /F m at salinities of 20–40 psu were always higher than those in other salinity treatments, rETR max reached maximal values at salinities of 20–30 psu, and qP peaked at salinities of 10–20 psu. For C. gracilis , the values of F v /F m at salinities of 5–40 psu were always higher than those at 1 psu or at 50–70 psu. The highest values of rETR max were also observed at salinities of 5–40 psu, whereas qP decreased slowly with increasing salinity from 10 to 60 psu. The changes in non-photochemical quenching (NPQ) were different in the two diatoms. For P . tricornutum , there were no significant differences below 60 psu for all three exposure times. Above 60 psu, however, NPQ in P . tricornutum increased with salinity up to 80 psu and decreased at 90 psu. For C. gracilis , NPQ decreased with increasing salinity from 1 to 20 psu, but increased at salinities of 20–70 psu during the 12- and 24-h periods, and was always low after 48 h. The specific growth rate of the two diatoms was inhibited at both low and high salinities, and decreased with increasing exposure times. The relative chlorophyll content of the two diatoms showed a similar trend to each other, with lower chlorophyll content occurring at extremely low and high salinities. These results indicated that extremely low and high salinity stress negatively influenced the chlorophyll fluorescence parameters and growth of these two diatoms.