Several species of harmful algal blooms (HAB) exert inimical effects on bivalve molluscs, with mass mortalities and pathologies reported worldwide. Information on the effects of HAB on the reproduction of bivalve molluscs, however, remains very limited. The Japanese pearl oyster Pinctada fucata martensii is an important economic species cultured in Japan. In previous studies, harmful dinoflagellates and raphidophytes were shown to affect embryos and larvae of Japanese pearl oyster. In the present study, quantitative deleterious effects of Alexandrium catenella, Alexandrium affine, Heterosigma akashiwo, and Chattonella marina on egg viability and spermatozoa swimming velocity are reported. All four HAB species significantly reduced the swimming velocity of spermatozoa. Egg viability was affected only after exposure to A. catenella and A. affine. An additional cytotoxicity test using Vero cells showed that bioactive exudates are associated with the deleterious effects and these effects are more prominent during the death phase of the algal culture. The results of the present study warrant further research on the effects of HAB species on gamete quality of bivalves, further characterization of bioactive compounds secreted by Alexadnrium spp., and highlight the role of physical activation of the toxic mechanism of harmful raphidophytes suggested in a previous study and confirmed in the present study.