In order to characterize the phylogenetic diversity of marine cyanophages, oligonucleotide primers were designed to specifically amplify ca. 592 bp fragments of the viral capsid assembly gene g20. Phylogenetic analysis of isolates revealed that cyanophages were highly diverse and widely distributed without significant geographical segregation. Cloning and sequencing analysis of 6 natural virus concentrates revealed 9 phylogenetic groups in 114 different g20 homologs. The structure of cyanophage communities in the estuary and the open ocean samples were different from each other, with unique phylogenetic clusters found for each environment. Changes in clonal diversity were also observed from surface waters to deep chlorophyll maximum (DCM) layer in the open ocean. Only three clusters contained known cyanophage isolates, while the identity of the other six clusters remained unknown. The high cyanophage diversity revealed by the g20 sequences suggests that marine viruses can potentially play important roles in regulating microbial genetic diversity.