The present article reviews the main achievements reached in bacterial genetics through the application of pulsed field gel electrophoresis. In particular, it summarizes the main subjects where the use of this technique has significant relevance for the analysis of bacterial genomes. With this purpose, it sums up some of the most relevant examples which illustrate the applicability of this technique in bacterial taxonomy, in epidemiological work and in the study of bacterial genome organization (including the assessment of the number of genomic elements and the size and topology of all of them). This technique, which makes it possible to make genomic comparisons in an easy, fast and repetitive way, has been demonstrated to be especially useful for those bacteria where the application of classical genetic techniques has not been possible.