Anthropogenic noise can have a negative effect on the physiology and survival of marine fishes. Most research has focused on later life-stages, and few studies have investigated the effects of human-induced noise on embryogenesis. The current study investigated whether playback of motorboat noise affected the embryogenesis of the coral reef damselfishes, Amphiprion melanopus and Acanthochromis polyacanthus. Embryos reared under the playback of boat noise had faster heart rates compared to the ambient reef controls. The effects of noise on morphological development differed between species and the fundamental interrelationships between early life history characteristics changed dramatically under boat noise for Ac. polyacanthus. Noise treatments did not alter the survival rates of embryos under laboratory conditions. Although species specific, our findings suggest that anthropogenic noise causes physiological responses in fishes during embryogenesis and these changes have direct impacts on their development and these alterations may have carry-over effects to later life stages.