Marine microbes and their viruses are essential parts of the marine ecosystem that form the base of the foodweb, and drive biogeochemical cycles. Studies have shown that marine viral communities display repeatable changes in abundance and community composition with time; however, whether these changes reflect shifts in dominance within evolutionarily related groups of viruses and their hosts is unexplored. To examine these dynamics, changes in the composition and phylogenetic makeup of two ecologically important groups of viruses, and their potential hosts, were followed at a coastal site near Vancouver, Canada, every two weeks for 13 months. Changes in the taxonomic composition within DNA bacteriophages belonging to the T4-like myoviruses and marine picorna-like RNA viruses infecting eukaryotic phytoplankton, as well as bacteria and eukaryotes, were followed using amplicon sequencing of gene fragments encoding the major capsid protein (gp23), the RNA-dependent RNA polymerase (RdRp) and the 16S and 18S ribosomal RNA genes, respectively. The results showed that the dominant groups of phylogenetically related viruses shifted over time, and that there were many transient and few persistent taxa. Yet, different community structures were observed for different marker genes. Additionally, with strong lagged correlations between viral richness and community similarity of putative hosts, the results imply that viruses influence the composition of the host communities, and that their community structure is dependent on lifestyle, cementing their role as important structuring elements in marine planktonic communities.