We investigated the ontogenic change in feeding habit of clams in natural waters based on chloroplast-targeting DNA metabarcoding. Samples of clams (spats, juveniles, adults), seawater and sediment were collected in three regions in Japan. We calculated compositions of diatom genera in each sample, proportions of planktonic and benthic diatoms in gut contents of clams and similarities of diatom genera compositions between each sample.