This review investigates the decline in sperm DNA quality in humans and various animal species, with a focus on sperm DNA fragmentation (SDF), its impact on reproductive outcomes, and its management in the context of assisted reproduction. The review underscores the significance of universally observed phenomena in human reproduction and proposes the application of insights gained from human studies to enhance reproductive strategies in animals and endangered species, where sperm quality research is limited and gametes for assisted reproduction are scarce. Universal aspects of the nature and origin of sperm DNA damage and repair are examined. It emphasizes the analysis of DNA breaks related to biological factors, such as histone-to-protamine exchange, oxidative stress, DNase activity, environmental pressures, and the unavoidable effects of iatrogenic DNA damage, particularly affecting processes related to assisted reproduction. The mechanisms underlying the repair of persistent DNA breaks that reach oocytes transported by sperm are also discussed. Methodologies for assessing SDF and differentiating between single- and double-stranded DNA breaks are explained. Various strategies to mitigate high levels of SDF in the ejaculate have been explored, and their potential applications in both humans and animal species have been discussed. A key conclusion is that SDF assessment offers valuable insights into semen quality, particularly in the era of assisted reproduction and specifically in intracytoplasmic sperm injection (ICSI), where traditional sperm parameters such as concentration, motility, and membrane quality evaluation are less critical. The causes of high SDF levels are multifactorial and complex, necessitating the establishment of standard protocols to control its negative effects on assisted reproduction. This is especially pertinent for endangered species, for which information on male fertility factors is limited. In humans, personalized treatment is essential to optimize the retrieval of high-quality gametes during fertilization. Similarly, assisted reproductive strategies for endangered species must be tailored to the specific sperm characteristics of each species. Various strategies to improve sperm DNA quality are now available, many of which are designed to mimic natural sperm behaviour shaped by evolutionary selection processes unique to each species. Exploring the synergistic effects of these strategies could enhance sperm availability and efficacy during fertilization.