Whole-genome paired-end sequencing library generated from high molecular weight genomic DNA extracted from young leaves of Argania spinosa. This library contributed to the de novo genome assembly (GenBank accession JCADCR010000000). Four genomic DNA sequencing libraries were generated from the same Argania spinosa individual using PCR-free library preparation and sequenced on the Illumina HiSeq 4000 platform (2  150 bp). All libraries were used collectively for de novo genome assembly.