To obtain basic ecological information on declining Tokyo Bay stocks of the Manila clam Ruditapes philippinarum, life history (including spawning, larval transport and settlement, and growth and survival of benthic clams) was investigated in local habitats, mainly in Sanbanse and Kisarazu. Spawning-stage adult clams were histologically detected from May to October at both sites, with two peak periods in summer and autumn. From May to November, between 13 and 23 larval cohorts appeared annually in each site, even during periods when spawning-stage adults were not detected. Spawning over many months plus larval transport from other habitats may contribute to the continuous appearance of larvae at both sites. This confirms the hypothesis that the clam population is maintained and supported by the reproduction of local populations. High density cohorts of newly settled clams, which later formed adult populations, may originate from larval cohorts spawned during peak spawning periods. A number of summer cohorts of benthic juveniles disappeared within 3–4 mo after settlement, whereas autumn cohorts maintained a relatively high density through the following spring, and subsequently they formed adult populations. Severe mortality resulting from extreme environmental factors may have affected the summer cohorts during summer and autumn. The recent decline of the adult stocks may be related to the unstable recruitment of summer cohorts, which was one of the two major seasonal components contributing to recruitment.