Neosiphonia savatieri, a filamentous red alga, had spread and caused a massive death of its host Kappaphycus alvarezii since March 2009 in China. With an aim to found a specific method to eliminate the N. savatieri efficiently from carrageenan producing K. alvarezii, the effects of glyphosate on the photosynthetic behaviors of K. alvarezii and N. savatieri were comparatively studied by using fast chlorophyll a (Chl a) fluorescence kinetics. A dose-and time-dependent changes of fast Chl a fluorescence kinetics were obtained in N. savatieri treated by glyphosate, meanwhile no significant change was detected in the K. alvarezii under the same treatment conditions. Moreover, the maximum PSII photochemical efficiency for dark-adapted tissues (F V /F m ) of N. savatieri decreased significantly when the N. savatieri was treated with glyphosate. Above results were further supported by transitory offshore glyphosate soak experiment. The brownish-red N. savatieri turned to be olivine then drew off within 5 days after soaking in >1 g L −1 of glyphosate for more than 1 min, meanwhile, no visible harmful effects were detected on K. alvarezii. Based on above results, glyphosate is suggested to be an effective chemical to eliminate N. savatieri from K. alvarezii.