Abstract. During the PeECE III mesocosm experiment in 2005 we investigated how the virioplankton community responded to increased levels of nutrients (N and P) and CO₂. We applied a combination of flow cytometry, Pulsed Field Gel Electrophoresis and degenerate PCR primers to categorize and quantify individual viral populations, and to investigate their temporal dynamics. Species specific and degenerate primers enabled us to identify two specific large dsDNA viruses, EhV and CeV, infecting the haptophytes Emiliania huxleyi and Crysochromulina ericina, respectively. Some of the viral populations detected and enumerated by flow cytometry did not respond to altered CO₂-levels, but the abundance of EhV and an unidentified dsDNA virus decreased with increasing CO₂ levels. Our results thus indicate that CO₂ conditions, or the related change in pH, may affect the marine pelagic food web at the viral level. Our results also demonstrate that in order to unravel ecological problems as how CO₂ and nutrient levels affect the relationship between marine algal viruses and their hosts, we need to continue the effort to develop molecular markers used to identify both hosts and viruses.