Marine ecosystems contain an immense diversity of phages, many of which infect the cyanobacteria responsible for a portion of oceanic primary productivity. To add to the growing body of research on the dynamics and diversity of these cyanophages, we measured cyanophage abundance, diversity, and community composition monthly for 15 mo at 3 coastal locations in Southern California, USA. We characterized over 900 individual cyanophages, isolated on Synechococcus sp. WH7803, by amplifying and sequencing 2 different genes from each isolate: g20 (the portal protein gene) and psbA (a host-derived gene involved in photosynthesis). The taxonomic composition and diversity of isolated cyanophages were highly variable over time, with little variation across the 3 locations. Particular taxa dominated the community at distinct times of year, with more rapid turnover of dominant types and higher overall abundance and diversity during spring and summer. These temporal patterns as well as taxonomic designations were highly congruent for both genes, based on operational taxonomic units (OTUs) defined at 99% nucleotide similarity, despite a greater level of amino acid conservation within psbA as compared to g20. Overall, this suggests that either gene can serve as a useful marker for cyanophage diversity. However, we detected 1 myovirus taxon (representing about 2.5% of the isolates) of uncertain phylogenetic affiliation that was negative for psbA amplification. Further sampling is necessary to assess whether these temporal dynamics in cyanophage composition, diversity, and abundance are seasonally recurring.