The population dynamics of lancelet Branchiostoma japonicum are reported for six sampling sites in the Seto Inland Sea, Japan, for November 2007–2016. Lancelet growth and life span varied spatially, being faster and shorter, respectively, at Stn 3 (off Marugame, western Bisan-seto) than at other sites; average body length at Stn 3 was 36.1 mm for 2-year-old lancelets, and 38.9–42.1 mm for 4-year-old lancelets at sites 1, 2, 4 and 6. Stepwise multiple regression analysis revealed adult growth rate to be significantly positively related to chlorophyll a concentration, and negatively correlated to lancelet density. Density of newly settled and adult lancelets varied spatially. Chlorophyll a concentration best predicted the density of newly settled lancelets, and sediment particle size best predicted that of adults, indicating that factors affecting lancelet density differ during their life history.