The era of whole genome sequencing has now firmly entered a new phase with the establishment of several technologies for deep or high-throughput sequencing. Consequently, we are now moving away from generating essentially finished, high quality reference genomes to functional genomics and the analysis of the phenotypic impact of genetic variation in populations. These changes are being felt in both the prokaryotic and eukaryotic worlds with consortia getting together to work on different large-scale projects. Examples include the sequencing of thousands of human genomes, which are being used to identify genes associated with classical phenotypes or disease. The analysis of the mouse is leading to large-scale gene knock-out programmes that eventually will cover all genes. The zebrafish genome will eventually direct similar gene knock-out programmes. In the case of bacteria (and viruses), which have relatively small genomes, the impact is being felt in multiple areas ranging from the analysis of RNA populations through to the molecular definition of phylogeny. A previous issue of Current Opinion in Microbiology (edited by Carmen Buchrieser and Stewart Cole) provided an editorial overview and several excellent reviews that reported on this field and here we extend the review coverage into other areas.