<p>The Y-chromosome, a hallmark of male-specific inheritance, holds immense importance in domestic animal genetics. It harbors the Sex-determining Region Y (SRY) gene, which initiates testis development and male differentiation. Due to its strict paternal inheritance and minimal recombination outside the pseudoautosomal regions (PARs), the Y-chromosome is a stable and reliable marker for studying male lineage, phylogeography, and patrilineal evolution in domestic species. Despite these constraints, advances in sequencing technologies and molecular tools (like Y-STRs and Y-SNPs) have enabled in-depth exploration of Y-chromosomal diversity. A comparative overview of the Y-chromosome architecture is presented for major domestic species, including cattle, sheep, goats, pigs, horses, dogs, and poultry. The genes present on the Y-chromosome are of growing interest in breeding programs to enhance male reproductive performance and disease resistance. Understanding Y-chromosome diversity is also critical for conservation genetics, especially in preserving indigenous breeds and managing genetic bottlenecks. This review also highlights the importance of Y-chromosome analysis in breeding strategies, particularly when combined with advanced tools. Studying Y-chromosome diversity provides valuable insights into male-driven domestication events. With the ongoing development of high-resolution molecular techniques, the scope for Y-chromosome-based research in domestic animals is expanding rapidly, promising to improve both scientific understanding and practical outcomes in animal breeding and conservation.</p>