Domestication and selection pressures have left specific genomic footprints known as selective sweeps, reflecting livestock adaptation to specialized production goals and diverse environments. This study aimed to conduct a comprehensive high-resolution genome-wide scan to identify genomic regions distinguishing dairy-type from beef-type native Iranian cattle. Genomic information from 90 native Iranian cattle across eight breeds (Sarabi, Kurdi, Mazani, Taleshi, Sistani, Kermani, Najdi, and Farsi), genotyped using the Illumina BovineHD BeadChip, was analyzed. Animals were categorized into dairy type and beef/dual-purpose type groups. After quality control, 278,667 SNP markers were retained for final analysis. Selection signatures were detected using pairwise Fst comparisons with theta (θ) method and a 5-SNP sliding window (Win5) approach. The comparative genomic scan for selection sweep identified 23 significant genomic regions, with the highest concentration of signatures on chromosomes 12 (five regions), 8 (five regions), and 13 (four regions). Win5 FST values ranged from 0 to 0.21. Functional analysis revealed 29 candidate genes including PLIN2 (lipid metabolism), RIMS1 (fertility), SLC24A2 (stress response), and GLP2R (energy metabolism). The identified regions showed significant overlap with documented QTLs for muscle growth, fertility traits, and milk composition. The results showed that despite the absence of industrial breeding programs in Iran's traditional livestock systems, centuries of human and environmental selection pressures have left deep genomic footprints in the genome of Iranian native breeds.