During a two year period 457 clones of the diatom Skeletonema costatum were isolated prior to and during the summer-fall and winter-spring blooms of this species in Narragansett Bay, R.I. Their allozyme banding patterns were examined for 5 enzyme loci. Genotypic frequencies indicated that the winter bloom populations were genetically different from the prevalent summer bloom populations of the same species. Genetic differences between seasonal blooms are as great as those found between species of terrestrial organisms, but are not accompanied by morphological variation. Although blooms have distinct prevalent forms, they are not genetically homogeneous. No single clone is ever representative of all populations of S. costatum. The dynamics of these allochronic populations appear to be governed by a form of cyclic natural selection, and are probably a regular feature of the cycles of abundance of this species in this area. These results cast doubt on some of the assumptions often made in the “autecological approach” to phytoplankton ecology. This study comprises the first quantitative examination of the population genetics of a microalga.