Fecundity, condition index, and gametogenic development of the Manila clam Ruditapes philippinarum were quantified at 2 sites on the intertidal fishing grounds of the Akkeshi-ko estuary, Hokkaido, Japan. In this study, an enzyme-linked immunosorbent assay was used to quantify the number of eggs in the clams. Fecundity and condition index were greater at the site with more availability of higher chlorophyll a concentrations and current velocities. However, histological analysis revealed that gametogenic development in the clams was completed at the site with lower food supply. The fecundity and condition index were limited in a part of this site, with high juvenile recruitment (>8,200 individual/m²) and intense food competition between the clams. Moreover, fecundity increased with size. The Akkeshi-ko estuary is located in northern Japan, where low temperatures mean sexual maturation progresses slowly in these clams. These results suggest that Manila clam fecundity increased through weight gain and repeated spawning could not occur due to their slow maturation.