Cyanobacteria of the genus Synechococcus dominates the prokaryotic component of the picophytoplankton in the oceans, contributing to a significant portion of total marine primary production. Cyanophage accounts for a significant Synechococcus mortality, and cyanophage lysis thus plays an important role in global carbon biogeochemical cycling. On the basis of  the  summarization of characterization of cyanophages including the hosts, phage families and lifestyles, this review described and discussed the methods, cyanophages distribution, genetic diversity and interaction with hosts. The  comparison of different gene markers which was widely used in cyanophage ecology was also presented. Finally we gave general outlook for the study of cyanophages, aiming to offer some references for the study of ecology of cyanophages and marine carbon cycling in the future.