Since the initation of the Global plan of action for Farm Animal Genetic Resources (FAnGR) in 2007, individual member countries, including Switzerland, should have started a monitoring program. In this context, we developed GenMon-CH, funded by the Federal Office for Agriculture (BLW), which is a WebGIS platform designed to monitor Swiss FAnGR and evaluate the degree of endangerment of livestock breeds. The system takes into account pedigree and introgression information, the geographical concentration of animals, the cryo-conservation plan and the sustainability of breeding activities based on socio-economic data as well as present and future land use conditions. A multi-criteria decision tool supports the aggregation of the multi-thematic indices mentioned above. It entirely relies on open source technologies. GenMon-CH allows users to upload pedigree-information (animal ID, parents, birthdate, sex, location and introgression) from a specific livestock breed and to define species and/or region-specific weighting parameters and thresholds. The program then completes a pedigree analysis and derives several indices that are used to calculate an integrated score of conservation prioritization for the breeds under investigation. The score can be visualized on a geographic map and allows a fast, intuitive and regional identification of breeds in danger. Appropriate conservation actions and breeding programs can thus be undertaken in order to promote the recovery of the genetic diversity in livestock breeds in need. The use of the platform is illustrated by means of an example based on three local livestock breeds from different species in Switzerland: the Braunvieh cattle breed, Franches-Montagnes horse breed and the Valais Blacknose sheep breed.