The present paper reviews the use of ecogeographical studies in the efficient conservation and utilization of plant genetic resources. While the use of genotypic information in agrobiodiversity studies has experienced a rapid boost during the last two decades, the use of environmental information on the collecting sites of the conserved germplasm (i.e., ecogeographical characterization) has gained importance in a more gradual way. Today we know that ecogeographical characterization reveals the adaptive range of species conserved and shows the most important environmental factors or variables for adaptation. Progress in ecogeographical characterization has been helped by the development and popularization of geographic information systems (GIS) software applications and environmental data arranged in layers compatible with such applications. GIS are useful to manage and analyze georeferenced data, such as passport collection data and environmental variables. Thus, GIS have become the best tool to perform ecogeographical analyses. Other related tools such as species distribution models or gap analysis can be easily integrated in ecogeographical analysis, offering improved results. As a result, GIS, related tools and ecogeographical analysis can be useful in a wide range of applications in the collection, conservation, characterization, documentation and utilization of plant genetic resources.