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The pangenome provides genomic variations in the cultivated gene pool for a given species. However, as the crop's gene pool comprises many species, especially wild relatives with diverse genetic stock, here we suggest using accessions from all available species of a given genus for the development of a more comprehensive and complete pangenome, which we refer to as a super-pangenome. The super-pangenome provides a complete genomic variation repertoire of a genus and offers unprecedented opportunities for crop improvement. This opinion article focuses on recent developments in crop pangenomics, the need for a super-pangenome that should include wild species, and its application for crop improvement.