We investigated the effects of salinity on the zoospore production of four mangrove thraustochytrid isolates, Schizochytrium sp. KF1, Aurantiochytrium mangrovei KF6, Thraustochytrium striatum KF9 and Ulkenia sp. KF13. The zoospore motilities, which were based on curvilinear velocity (VCL) and straight-line velocity (VSL), were monitored using the Computer-Assisted Sperm Motility Analysis (CASA) Software system. The zoospore production of four isolates was suppressed at salinity above 15%. Schizochytrium sp. produced the greatest number of zoospores at 15%, while Aurantiochytrium mangrovei and Ulkenia sp. produced abundant zoospores in diluted sea water ranging from 7.5 to 15%. Thraustochytrium striatum performed relatively poorly under all salinities. Salinity and exposure time, as well as their interactions, had significant impacts on most zoospore velocity measurements. The optimal velocities of zoospore motility also varied among isolates. Zoospores of Schizochytrium sp. and A. mangrovei had similar responses to salinity, with the highest motility at 7.3%, followed by a decrease in velocities with increasing salinity. In contrast, the zoospore of T. striatum had optimal motility at 12% and remained highly motile from 15 to 20%. The velocities of zoospores of Ulkenia sp. were the lowest among the tested thraustochytrids and had optimal motility at 12%. Zoospores of all the isolates remained active after 4 h of exposure to aqueous medium, but the optimal salinity for each mode of swimming changed. The ecological significance of these data are discussed.