The Neotropics, encompassing Central and South America, stand out for their extraordinary biodiversity and cultural richness. Indigenous Americans exhibit remarkable cultural and linguistic diversity, but their genetic diversity is among the lowest among human populations. Environmental factors, including altitude, temperature, and biodiversity, have influenced the genetic makeup of Indigenous Americans since the earliest peopling of the America. Additionally, human impact, such as hunting, harvesting, and wildlife management, has significantly affected neotropical biodiversity. Niche construction, driven by plant and animal domestication and landscape modification, has played a crucial role in agriculture and has heavily influenced the genetic diversity of the region. The interplay between humans and their environment has shaped human genetic adaptations concerning diet and susceptibility to infectious diseases, affecting contemporary indigenous and admixed populations. Furthermore, migrations have played a significant role in shaping the genetic structure of neotropical human populations. Over time, multiple migration waves have contributed to the genetic diversity observed in present-day populations. The peopling of the America involved successive migrations dating back at least 15,000 years, followed by later post-contact migrations from various world regions. The study of genetic variation in neotropical populations has provided insights into their evolutionary history, demographic changes, and the impact of historical events like colonization and the transatlantic slave trade. Understanding the complex interplay of genetic, environmental, and historical factors is vital for conserving the biodiversity of humans and ecosystems. This chapter discusses the importance of migrations, demographic changes and natural selection in shaping the genetic diversity of neotropical human populations.