Using CsCI-Hoechst dye or CsCI-ethidium bromide gradients, satellite and nuclear DNAs were separated and characterized in three marine dinoflagellates: Glenodinium sp., and two toxic dinoflagellates, Protogonyaulax tamarensis and Protogonyaulax catenella. In all three dinoflagellates, the lowest density fraction, satellite DNA1, hybridized to chloroplast genes derived from terrestrial plants and/or other algae. Dinoflagellate chloroplast DNAs exhibited molecular sizes of 114 to 125 kilobase pairs, which is consistent with plastid sizes determined for other chromophytic algae (120-150 kilobase pairs). Mitochondrial DNA was not resolved from nuclear DNA in this system. Two additional satellite DNAs, satellite DNA2 and satellite DNA3, recovered from P. tamarensis and P. catenella were similar to one another, both within and between species, when characterized by restriction enzyme analysis. These satellites were 85 to 95 kilobase pairs in size, and exhibited restriction fragments that hybridized to yeast nuclear ribosomal RNA genes. Restriction enzyme analyses and DNA hybridization studies of cpDNA document that the two Protogonyaulax isolates are not evolutionarily identical.The Dinophyceae is a group of unicellular, eukaryotic organisms that is composed of photosynthetic, heterotrophic, phagocytic, and saprophytic forms. These algae are second only to diatoms in their contribution to primary production in marine and freshwater ecosystems. In addition, species of photosynthetic dinoflagellates have been identified as the dominant organisms comprising the toxic "red tides" that periodically close shellfish aquaculture facilities on both the East and West Coasts.Dinoflagellates possess unique DNA characteristics. Cells of this taxonomic group frequently contain very high levels (32-200 pg/cell) of DNA packaged into chromosomes that lack classic histone-like proteins. These chromosomes remain condensed throughout cellular interphase (28) and contain an '