Viruses in Earth's aquatic environment outnumber all other forms of life and carry a vast reservoir of genetic information. A large proportion of the characterized viruses infecting eukaryotic algae are large double-stranded DNA viruses, each of their genomes carrying more than a hundred genes, but only a minority of their genes resemble genes with known biological functionalities. Unusual forms of single-stranded DNA and single- and double-stranded RNA viral genomes have been characterized over the last 10 years, and the number of novel taxa of viruses being discovered continues to increase. Although viral infections are usually specific to certain host strains in a species, lytic viral infections nevertheless affect a large proportion of algae and have a global impact, for example in the termination of blooms. Resistance to viruses is thus subject to strong selection, but little is known about its mechanism. Lateral gene transfer between host and virus has been shown by comparisons between their complete genomes and must play an important role in coevolution in the microbial world. Recent advances in bioinformatics and the possibility of amplifying complete genomes from single cells promise to revolutionize analyses of viral genomes from environmental samples.