Persian or English walnut (Juglans regia L.), the walnut species cultivated for nut production, is one of the oldest food sources known and is grown worldwide in temperate areas. In this work, genotyping resources have been developed for two works. Firstly, SSR genotyping has been done using 13 SSR markers, for 253 accessions of the INRAE's Walnut Genetic Resources. These data have been processed in order to assess genetic diversity and structure of the collection. The raw SSR genotyping datafile is in "tab" format and the informations related to the SSR loci are in "txt" format. Secondly, SNP genotyping has been done using the Axiom 700K J. regia SNP array, for 170 accessions of the INRAE's Walnut Genetic Resources. These data have been processed in order to do Genome-Wide Association Study. Moreover, a F1 progeny of 78 individuals from a cross between 'Franquette' and 'UK 6.2' was also genotyped with the array, in order to do QTL mapping. The two raw SNP genotyping "txt" datafiles are in "hapmap" format. A "csv" file is also added to make the link between the ID of Axiom array and the IDs of the INRA's Walnut Genetic Resources (https://doi.org/10.15454/58SYJV).