A 7000-year record of Coccolithovirus and its host, the calcifying haptophyte Emiliania huxleyi, was reconstructed on the basis of genetic signatures preserved in sediments underlying the Black Sea. The data show that the same virus and host populations can persist for centuries. Major changes in virus and host populations occurred during early sapropel deposition, similar to 5600 years ago, and throughout the formation of the coccolith-bearing sediments of Unit I during the past 2500 years, when the Black Sea experienced dramatic changes in hydrologic and nutrient regimes. Unit I saw a reoccurrence of the same host genotype thousands of years later in the presence of a different subset of viruses. Historical plankton virus populations can thus be included in paleoecological and paleoenvironmental studies.