The Neotropical region is renowned for its high biodiversity but also faces numerous threats to their species, with many of them at risk of extinction. Population decline of several species are often due to human-driven factors such as habitat loss and degradation, overfishing, and illegal wildlife trafficking. Conservation genetics has the potential to aid information in assessing the conservation status, monitoring populations through non-invasive methods, delineating conservation units within species, and unraveling the biodiversity obscured by cryptic species. Moreover, it can provide important information applicable to translocation and ex-situ conservation initiatives, and relevant for combating illegal wildlife traffic. Throughout this chapter, we present a range of conservation genetic strategies employed in diverse efforts to preserve animal populations within the neotropical region. We also examine their limitations and propose the integration of recent genomic advances and interdisciplinary approaches to pave the way for more innovative conservation approaches.