<p>Walnut (<i>Juglans</i> spp.) is a significant nut crop valued for its high nutritional content and commercial timber. Cultivated across temperate zones, walnuts exhibit extensive genetic diversity, encompassing wild genotypes and commercial cultivars. This review highlights the utility of molecular markers and advanced omics technologies, such as next-generation sequencing (NGS), genotyping by sequencing (GBS), genome-wide association studies (GWAS), and quantitative trait loci (QTL) mapping, in characterizing walnut germplasm and accelerating breeding efforts. These tools facilitate the identification of key genomic regions associated with desirable agronomic traits, enhancing breeding precision. Key traits targeted in breeding programs include lateral bearing, late leafing, early harvest, and resilience to biotic and abiotic stressors. The integration of genomic selection and marker-assisted breeding has improved selection efficiency, reducing the time required to develop superior cultivars. The review also discusses genomic advancements, including structural and functional studies, to elucidate the genetic mechanisms underlying elite traits. Functional genomics explores gene networks linked to growth and development, stress tolerance, nutritional and medicinal properties, and specialized metabolites production gene, providing a roadmap for genomics-assisted breeding. Emerging biotechnological approaches, such as CRISPR-based genome editing and transcriptomic analysis, are further refining walnut breeding strategies by enabling precise modifications of target genes. These advancements are paving the way for developing high-yielding, stress-tolerant walnut cultivars to meet the demands of modern agriculture. Additionally, conservation genomics is gaining importance in preserving walnut genetic resources, ensuring the sustainability of breeding programs and maintaining biodiversity for future genetic improvements.</p>