Simple Summary: The process of semen cryopreservation can have multiple advantages in an ex situ conservation program. However, there is a necessity to adapt the protocol to the specificity of each species. With that in mind, we aimed to optimize the sperm freezing/thawing process and study the effect of different cryoprotectants in the peregrine falcon.Abstract: Sperm cryopreservation is a complex process that needs to be adapted to wild and domestic avian species to ensure proper efficiency. Because of its accessibility, the peregrine falcon may be used as a good model for studying other raptor species. To find the most optimal cryopreservation protocol for peregrine falcon ejaculates, sperm parameters such as motility, viability, DNA fragmentation, acrosome integrity, and mitochondrial activity were analyzed under different conditions by varying the freezing method (slow freezing in straws vs. ultrarapid freezing in pellets), thawing conditions (37 • C for 30 s vs. 5 • C for 1 min), type of cryoprotectant (DMA vs. DMSO), and concentration of DMSO (4% vs. 8%). Results show that slow cryopreservation in straws yielded greater percentages (p < 0.05) of motile spermatozoa (22.5% ± 4.4% vs. 0.0% ± 4.1%), viable spermatozoa with intact acrosomes (84.6% ± 4.3% vs. 77.4% ± 4.3%), and spermatozoa with active mitochondria (41.0% ± 6.7% vs.12.8% ± 6.7%), compared with those obtained by the ultrarapid freezing in pellets. However, no differences were found between different thawing conditions. Moreover, all sperm motility parameters were greater (p < 0.05) when DMSO was used during freezing compared with DMA, although the use of 3% and 8% DMSO produced similar results. In conclusion, these results represent important progress in the study of falcon semen cryopreservation protocol, highlighting the crucial steps of the process and the most suitable conditions. Animals 2020, 10, 691 2 of 11 existent species. A viable presented solution is the creation of a germplasm bank that contains the sperm, oocytes, or even embryos of the largest possible number of species [2,3].Since the storage of eggs or embryos from birds poses a difficult challenge because of their large size and complexity, sperm cells are a good alternative [4]. Sperm is fairly easy and inexpensive to acquire, and its cryopreservation is much more accessible compared with the oocyte/embryo, because of the small volume of water inside of the sperm [5]. Furthermore, existing technologies allow the semen of many animal species to be collected and used [6]. Frozen semen can be a very important part of ex situ conservation efforts, since it allows for the storage of genetic material from multiple species for a long period of time. Stored semen can be used in reintroduction projects or to enlarge the genetic pool of a fragmented population. It also allows for the selection of individuals of genetic interest and the exchange of samples between distant locations [7,8]. In birds, frozen semen could become an increasingly relevant tool, because captive breeding programs a...