By frequent sampling from May 2001 to October 2002, we examined spatio-temporal variations in densities of different life stages (planktonic larvae, new settlers and small, large and commercial individuals) of Corbicula japonica in the Kiso estuaries (the Ibi-Nagara Estuary and the Kiso Estuary). Planktonic larvae were found for a much longer period (mainly in June to December 2001 and in April to October 2002) than reported in previous studies. Densities of planktonic larvae were significantly higher in the Kiso Estuary than in the Ibi-Nagara Estuary, whereas the reverse was true for new settlers and commercial individuals, indicating that larval settlement processes may be critical in establishing significant differences in the density of benthic stages between these estuaries. Ontogenetic habitat shift of the clam was detected in the Ibi-Nagara Estuary but not in the Kiso Estuary: the main habitats for new settlers and small individuals were located in the upper parts of the Ibi-Nagara Estuary and large and commercial individuals were located in the middle part. On the other hand, in the Kiso Estuary, all life stages from new settlers to commercial individuals were found mainly in the upper part. The above distribution patterns of C. japonica were much different from those of 3 other bivalves (Ruditapes philippinarum, Musculista senhousia and Mactra veneriformis) that are also common and abundant in these estuaries: high densities of these 3 bivalves were always found around the river mouths throughout their ontogeny.