Restriction fragment length polymorphisms (RFLP's) were examined in three strains of the marine diatom Skeletonema costatum using higher plant chloroplast and nuclear gene probes. Two of the strains, isolated from Narragansett Bay, RI, are representative of different allochronic seasonal populations. The third is a standard strain of this species obtained from the culture collection of marine phytoplankton. DNA hybridization probes revealed RFLP's among these strains, a finding which is consistent with an earlier hypothesis that local population diversity has a genetic basis. The large number of DNA polymorphisms observed indicate that a systematic revision of this genus using molecular approaches should begin with population-level studies. A method for the extraction of high molecular weight DNA from diatoms and other microalgae is reported.