Semen quality traits, including sperm morphology, sperm shape, sperm count, ejaculate volume, low percentage of motile spermatozoa in semen, and motility, play a crucial role in male reproductive efficiency and fertilization success. This review article highlighted the impact of genetic polymorphisms in genes on semen quality and fertility traits in mammalians. Single nucleotide polymorphisms (SNPs) in these genes were associated with various sperm abnormalities, such as abnormal sperm flagella morphology, reduced motility, impaired DNA integrity, altered antioxidant status, disrupted sperm head–tail junction, spermatogenesis defects, reduced testicular size, and a range of sperm disorders. This comprehensive review of the available literature offers significant insights into the genetic factors influencing semen quality traits, which can contribute to the development of genetic markers and the enhancement of male fertility through assisted selective breeding programs.