Metagenomic studies have revealed the unexplored diversity of the environmental virosphere. However, most studies are biased towards specific types of viral genomes due to the absence of universal methods to access all viral genome types. In the present study, we established a novel system to efficiently separate single- and double-stranded DNA/RNA viral genomes using hydroxyapatite and cellulose chromatography. This method will allow us to quantitatively and simultaneously access four types of viral genomes and will provide important clues to further understand previously unexplored environmental viral populations and obtain potentially unbiased libraries from environmental viral communities.