High-throughput sequencing makes it possible for the first time to sequence hundreds of microbial genomes rapidly at low cost. These methods have huge potential to significantly improve our understanding of microbial evolution, so that many research projects have recently been set up to generate and analyze such data. This symposium will provide an overview of the progress made by such projects, as well as the many challenges they pose. It is now possible to identify the vast majority of SNPs within large population samples of microbial isolates. These datasets are illuminating the molecular, ecological and population-level dynamic processes occurring over short time scales in natural populations inhabiting a range of habitats from the clinic to the environment. We aim to  explore these recent advances and the development of new methods of analyses required to fully exploit these extremely large sequence datasets. Relevant topics include quantifying the variation in the rates of recombination and mutation between closely related lineages, the evolution of base composition, the relative power of drift and selection, examining the acquisition of adaptive traits (e.g. antibiotic resistance, host adaptation, metabolic flexibility, regulatory changes) within a phylogenetic framework, and the distribution of variation over time and space (phylogeography). The role of phage and conjugative elements in structuring populations as both vehicles for gene flow and parasitic elements will also be considered. The symposium will focus on variation within natural populations rather than experimental evolution.