We studied renewal of genetic composition of a lancelet, Branchiostoma belcheri, at a station in the Seto Inland Sea, Japan, using random amplified polymorphic DNA (RAPD) technique. We detected a total of 49 DNA bands from 27 individuals of 5 seasonal samples. Among these, some were specific to individual or seasonal sample. There were no bands common to all individuals. We calculated the Band Sharing Index (BSI) values for each combination of individuals. BSI was in a wide range of 0.00–0.97 and the average BSI between the individuals of a sample was remarkably different from sample to sample (0.37–0.83). In cluster analysis on the basis of BSI, largely 3 clusters were constructed, which finally connected to a single cluster at as low as about 0.2 of BSI. Besides, many clusters were constructed exclusively by a seasonal sample. These results suggest a large gene pool of lancelets in this area, the remarkable differences in gene pool size among the samples and a seasonal renewal of genetic composition at a habitat.