This study examined a new method of mitigating harmful algal blooms (HABs) by combining biosurfactant sophorolipid and yellow clay. To investigate the effects and practicability of this HAB mitigation method, field experiments were carried out during a Cochlodinium bloom near Miruk Island, South Korea, in August 2002. Field experiments examined the effects of sophorolipid and yellow clay on Cochlodinium bloom mitigation and on marine plankton such as bacteriaplankton, heterotrophic protists, and zooplankton. A mixture of 5 mg l −1 sophorolipid and 1 g l −1 yellow clay was sprayed directly on the sea surface and its effect was compared with that of 10 g l −1 of yellow clay applied under similar conditions. The sophorolipid–yellow clay mixture more efficiently mitigated the Cochlodinium bloom (95% removal efficiency after 30 min) than yellow clay alone (79% after 30 min). Further, no variation in bacterial abundance occurred 30 min after spraying the sophorolipid–yellow clay mixture. After 30 min, heterotrophic protist abundance at the surface decreased 21 and 41%, respectively, following the sophorolipid–yellow clay mixture and yellow clay treatments. Zooplankton decreased by 38% 15 min after spraying the mixture and 67% 30 min after spraying the yellow clay. These results indicate that the mixture of sophorolipid and yellow clay had a less adverse effect on bacteriaplankton, heterotrophic protists, and zooplankton than the yellow clay, suggesting that the sophorolipid–yellow clay mixture can mitigate HABs efficiently with fewer negative effects on the pelagic ecosystem.