There is great concern about the ecological impacts and benefits of oyster culture on estuaries and coastal waters. To examine the effects of the system-scale removal of oyster culture racks on phytoplankton and periphyton in a eutrophic tropical lagoon, a long-term study was conducted at 2 to 3 mo intervals from June 2000 to June 2004 (includes the time of complete oyster culture removal from Tapong Bay, southwestern Taiwan in June 2002). The abundances, productivities, and community structures of the inner (poorly flushed) and outer (well flushed) regions were compared before and after rack removal. Tidal flushing was an important factor regulating the responses of phytoplankton. After rack removal, mean chlorophyll a and maximum gross production (GP max ) rate of phytoplankton increased 4-fold in the inner region, but remained unchanged in the outer region and at the control site. Phytoplankton communities in both regions and at the control site were dominated by Bacillariophyta alone before rack removal, but shifted to a co-dominance of Bacillariophyta, Dinophyta, and Cyanobacteria after rack removal. When GP max rate was normalized to chl a (P B max ) and expressed as maximum photosynthetic intensity, no significant difference was detected before and after rack removal in either region. Chl a accumulation rate, GP max rate, P B max , and dominant species of periphyton did not differ significantly before and after rack removal in either region. Our results suggest the effectiveness of top-down control of phytoplankton abundances and a reduction in community diversity by cultured oysters in this eutrophic lagoon.