Sequencing DNA from single cells has opened new windows onto the microbial world. It is becoming routine to sequence bacterial species directly from environmental samples or clinical specimens without the need to develop cultivation methods. Recent technical improvements often allow nearly complete genome assembly from these otherwise inaccessible species. New bioinformatics methods are also improving genome assembly from single cells. The use of single-cell sequencing in combination with metagenomic analysis is also emerging as a powerful new strategy to analyse bacterial communities. Here, the technical developments that have enabled single-cell sequencing, as well as some of the most exciting applications of this approach from the past few years, are reviewed.