The genetic diversity of a phytoplankton population is important in determining the response to changing environmental conditions. This diversity may also be important for bloom formation. We have examined the genetic diversity of Skeletonema marinoi clones isolated from Gullmar Fjord on the Swedish west coast. This is a very common species in the planktonic community of the area. It occurs from February to November, and reaches its highest density during the spring bloom in February or March. Different clones were individually isolated from plankton samples collected over the range of more than one year. Sequencing of conserved parts of the genome (LSU rDNA) displayed a range of genetic variation, whereas morphological features examined in electron microscope did not vary. Allellic diversity within the population was confirmed by analyzing microsatellite loci. Genetic variation indicates that sexual reproduction is important in the population. High genetic diversity of the population may be a prerequisite for its extensive occurrence during variable seasonal conditions.