Cyanophages are a group of viruses infecting the cyanobacteria, and are widespread in both marine and freshwater environments. As important components of microbial communities,cyanophages play significant roles in cyanobacterial population structure and diversity and aquatic ecological environments. yanophages contain some host-like metabolic genes, as to auxiliary metabolic genes, which encode proteins involved in the light reactions of photosynthesis, pentose phosphate pathway, nutrient acquisition and DNA biosynthesis during the process of infecting cyanobacteria. Recently, some auxiliary metabolic genes have been used as target genes for investigating cyanophage diversity, and the interactions between cyanophages and nobacteria. In this review, we summarized advances in studying the origin, biological function and genetic diversity of cyanophage auxiliary metabolic genes at home and abroad.