The field of viral ecology has long endeavored to devise and adapt methodologies to peer beyond the visible and elucidate the roles of viruses in the environment. Much has been learned regarding the dynamics of viral assemblages and the significant role viruses have in biogeochemical cycles (Brussaard et al., 2008). Despite these advances, detailed under- standing of biological processes behind ecosystem- scale effects of viral infection has remained largely obscured, with research relegated to a handful of available host–virus culture systems. Increasingly affordable DNA sequencing has provided a route to assess the genetic diversity of viruses in the environ- ment. Current research seeks to apply genomic technologies to address knowledge gaps in environ- mental virology, but obstacles presented by the unique biology of viruses must be addressed to understand the context and significance of viral genome and metagenome sequence data. Coincident with the twentieth anniversary of the publication that launched the field (Bergh et al., 1989), viral ecologists from around the world met in 2009 for a workshop of the Scientific Committee for Oceano- graphic Research (SCOR) Working Group on the Role ofVirusesinMarine viral-ecology.dbi.udel.edu) and at a session entitled ‘From Direct Counts to Metagenomics: Two Decades of Discovery in Aquatic Viral Ecology’ at the 109th General Meeting of the American Society for Micro- biology (ASM; http://www.asm.org). These meetings covered a broad range of topics relevant to environ- mental virology, however, the impact of metagenomics emerged as a major topic. Highlighted are important issues for viral metagenomics raised during a round- table discussion (SCOR) and through various abstracts presented at both forums.