We studied the temporal succession of vertical profiles of Emiliania huxleyi and their specific viruses (EhVs) during the progression of a natural phytoplankton bloom in the North Sea in June 1999. Genotypic richness was assessed by exploiting the variations in a gene encoding a protein with calcium-binding motifs (GPA) for E. huxleyi and in the viral major capsid protein gene for EhVs. Using denaturing gradient gel electrophoresis and sequencing analysis, we showed at least three different E. huxleyi and EhV genotypic profiles during the period of study, revealing a complex, and changing assemblage at the molecular level. Our results also indicate that the dynamics of EhV genotypes reflect fluctuations in abundance of potential E. huxleyi host cells. The presence and concentration of specific EhVs in the area prior to the bloom, or EhVs transported into the area by different water masses, are significant factors affecting the structure and intraspecific succession of E. huxleyi during the phytoplankton bloom.