Techniques involving whole-genome sequencing and whole-population sequencing (metagenomics) are beginning to revolutionize the study of ecology and evolution. This revolution is furthest advanced in the Bacteria and Archaea, and more sequence data are required for genomic ecology to be fully applied to the majority of eukaryotes. Recently developed next-generation sequencing technologies provide practical, massively parallel sequencing at lower cost and without the requirement for large, automated facilities, making genome and transcriptome sequencing and resequencing possible for more projects and more species. These sequencing methods include the 454 implementation of pyrosequencing, Solexa/Illumina reversible terminator technologies, polony sequencing and AB SOLiD. All of these methods use nanotechnology to generate hundreds of thousands of small sequence reads at one time. These technologies have the potential to bring the genomics revolution to whole populations, and to organisms such as endangered species or species of ecological and evolutionary interest. A future is now foreseeable where ecologists may resequence entire genomes from wild populations and perform population genetic studies at a genome, rather than gene, level. The new technologies for high throughput sequencing, their limitations and their applicability to evolutionary and environmental studies, are discussed in this review.