Although large DNA viruses of eukaryotic algae represent a major force in shaping populations of plankton, knowledge about them is often limited to their overall diversity, abundance, and the flux of their constituent matter between ecosystem compartments. In order to gain insight about the genetics and structure of such populations, we used an easily cultivable model unicellular algal species, Ostreococcus tauri (Prasinophyceae), to monitor and compare populations of viruses in different marine environments. The abundance of O. tauri viruses showed very large temporal fluctuations, but remarkably was more than two orders of magnitude higher in lagoons than in coastal waters. We analysed 161 individual viruses found after plating out for lysis plaques on the host during a time series of water samplings. The haplotypes of viruses infecting our host strain were determined by sequence analysis of the partial DNA polymerase gene, permitting a spatiotemporal analysis of their population structure. We found 48 haplotypes, only the two most abundant ones being shared among all of the three study sites (lagoon, coastal and offshore), supporting the hypothesis that there is great diversity among the viruses infecting one host strain. However, our data suggest that the population structure differ between lagoons and coastal sea.