Abstract Motivation Understanding the molecular evolutionary history of organisms usually requires visual comparison of genomic regions from related species or strains. Although several applications already exist to achieve this task, they are either too old, too limited, or too complex for most user’s needs. Results GenoFig is a graphical application for the visualization of prokaryotic genomic regions, intended to be as easy to use as possible and flexible enough to adapt to a variety of needs. GenoFig allows the personalized representation of annotations extracted from GenBank files in a consistent way across sequences, using regular expressions. It also provides several unique options to optimize the display of homologous regions between sequences, as well as other more classical features such as sequence 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 in prokaryotes and to produce publication-ready figures. Availability and implementation Genofig is fully available at https://forgemia.inra.fr/public-pgba/genofig under a GPL 3.0 license.