GnpIS is a modular and interoperable Information System for plant and pest genomics (http://urgi.versailles.inra.fr/gnpis). It is a powerful multispecies centralized information system with seven linked relational databases. GnpIS is designed to bridge different kinds of data, from the accessions or genotypes to their phenotypic, genetic or genomic characterization for species of agronomical interest. It is used as an international repository for Wheat Genomic data (International Wheat Genome Sequencing Consortium repository), a key component of the information system of the French national infrastructure for phenotyping (https://www.phenome-fppn.fr/) and is a key resource for several important French private-public initiatives on crops (maize, wheat, sunflower, pea, rapeseed, energy crops). The system is being made interoperable with other similar infrastructures at the national level through the IFB plant node project, at the European level through the TransPLANT and ELIXIR infrastructures and at the international level through the Wheat Initiatiative. GnpIS offers a virtual access through a web portal (https://urgi.versailles.inra.fr/gnpis/) and different tools for searching: a google like quick search tool, whole portal advanced query tools (Intermine, Biomart, Galaxy) and specific interfaces for queries in each modules of the database.