Most concerns about antibiotic resistance are linked to the extremely efficient dissemination of mobile genetic elements carrying resistance genes, such as plasmids and conjugative transposons. Understanding the evolution of these elements usually requires visual comparison of replicons hosted by various bacterial strains or species. Here we present GenoFig, a graphical application for the generation of comparative genomics figures, intended to be as easy to use as possible for biologists and flexible enough to adapt to a variety of needs. GenoFig allows the personalized representation of annotations extracted from GenBank files in a consistant way across sequences, using regular exressions. It also provides several unique options to optimize the display of homologous regions between sequences, as well as other more classical features such as GC percent or GC-skew representations. In summary, GenoFig is a simple, free, and highly configurable tool to explore the evolution of specific genomic regions and to produce publication-ready figures.