This dataset provides the full genome annotation supporting the publication: "Phased T2T reference genome assembly of Moroccan Argane (Argania spinosa)"Hanane El Idrissi, Anestis Gkanogiannis, Driss Iraqi, Siham Khoulassa, Mohamed Fokar, Bouabid Badaoui, Rachid Moussadek, Rachid Mentag and Slimane Khayi (2025) We present the genome annotation files for the phased, telomere-to-telomere (T2T), chromosome-scale genome assembly of Argania spinosa, an ecologically and economically important tree endemic to Morocco. The assembly comprises two fully phased haplotypes, each organized into 11 pseudochromosomes. This Zenodo entry includes: Structural gene annotation (GFF3) generated using the Funannotate pipeline Predicted protein sequences (FASTA) Repeat annotations: GFF3 files for simple, complex, and combined repeat annotations Soft-masked genome FASTA (simple and complex repeats masked in lowercase) Hard-masked genome FASTA (repeats replaced with Ns) Gene prediction was performed using transcript evidence (RNA-Seq from root and leaf tissues), protein homology from Ericales and SwissProt, and de novo ab initio models (AUGUSTUS, GeneMark-ES). Functional annotations were assigned using InterProScan, eggNOG, Pfam, and Gene Ontology databases. Repeat annotation was performed using RepeatModeler and RepeatMasker in a multi-round strategy incorporating both lineage-specific and de novo repeat libraries. NCBI BioProject: PRJNA1223813