The effects of four harmful and potentially harmful dinoflagellates, Alexandrium affine, Alexandrium catenella, Karenia mikimotoi and Karenia papilionacea, on the early-life development of Japanese pearl oyster, Pinctada fucata martensii, were assessed. Density- and time-dependent, mild to severe effects on cleavage, hatching, D-larvae, and pre-settling larvae of pearl oysters were found. The non-PST-producer A. affine was highly toxic to both cleavage and hatching with potent lytic activity at a density of 2.5×102cellsml−1. The PST-producer A. catenella also affected cleavage and reduced hatching, but at 2-fold higher density with lytic activity only at the highest density tested (2×103cellsml−1). Cleavage was affected by K. mikimotoi and K. papilionacea at 1.5×104cellsml−1, but hatching was only affected by K. mikimotoi. Mortalities in both larval stages were not observed. D-larvae were not affected by K. papilionacea, but their activity decreased following exposure to A. affine, A. catenella, and mainly K. mikimotoi. Pre-settling larvae were more sensitive to all four harmful algae than were D-larvae. The dinoflagellate A. catenella had the highest effect on the activity of pre-settling larvae (10cellsml−1), followed by K. mikimotoi (5×102cellsml−1), A. affine (5×102cellsml−1), and K. papilionacea (1.5×104cellsml−1). The results of this study suggest that complex mechanisms, including paralytic shellfish toxins (PST), brevetoxins (PbTx) and a variety of lytic and membrane-disruptive toxins and/or other metabolites, could have been involved in such inimical stage-specific effects. It also highlight the threat posed by harmful algae on the recruitment of Japanese pearl oysters and potentially other bivalve species, and show that they could exert subchronic to chronic effects at realistically low cell densities, and impact bivalve populations through altered reproductive and recruitment processes, ultimately hampering both wild populations and aquaculture industries.