Allelopathic effects of fresh tissue and dry powder of a nonsexual and a sexual strain of the macroalga Ulva pertusa on the growth of the microalgae Heterosigma akashiwo and Alexandium tamarense were evaluated using long-term coexistence culture systems in which several concentrations of macroalga fresh tissue and dry powder were used. The effects of macroalga culture medium filtrate on the two HAB algae were also investigated. Moreover, isolation co-culture systems were built to confirm the existence of allelochemicals and preclude the growth inhibition by direct contact. Short-term algicidal effect assays of macroalgae on H. akashiwo were carried out to measure the rate of algal cell lysis. The results of the coexistence assays showed that the growth of H. akashiwo and A. tamarense was strongly inhibited by fresh tissue and by dry powder of both strains of U. pertusa. The allelochemicals were lethal to H. akashiwo at relatively higher concentrations. The macroalga culture medium filtrate exhibited no apparent growth inhibitory effect on the two HAB algae under initial or semicontinuous filtrate addition, which suggested that continuous release of small quantities of rapidly degradable allelochemicals from the fresh tissue of both strains of U. pertusa was essential to effectively inhibit the growth of H. akashiwo and A. tamarense.