Gene flow is the movement of genes among and within populations of a species, which can occur in time and space. The process by which individuals (alleles) enter or leave a population is known as migration and is more common in animals. Thus, these evolutionary factors are determinants of the genetic diversity within and among populations. In this chapter, we introduce basic concepts of populations related to the genetic basis and the importance of gene flow in the survival and reproduction of plant species. The influence of gene flow and migration on the genetic diversity of these populations and their consequences are addressed. In neotropical trees, gene flow occurs through the dispersal of pollen (contemporary) and seeds (historical) dispersal, carried out by animals or by the action of physical factors such as wind and water. An effective gene flow depends on the number of genes and the genetic divergence of the participating populations, as well as on the dispersal agents. Migration is the change in the constitution of the population and the ecosystem. Migration is more noticeable in animal populations compared to plants, which require a longer time for such changes to become evident. As examples, we briefly discuss the knowledge about gene fluctuations in case studies of two types of populations: (i) natural populations; (ii) aroeira genebanks (AGB). In the first case, there is no anthropic interference, and it allows for a better understanding of how gene fluctuations occur in natural populations. In AGB there is a higher frequency of certain (favorable) alleles, in other words, a direction in the gene flow has been directed through human intervention. The importance of migration in the biodiversity of biomes and colonization of some plant species are also discussed. Perspectives on the usefulness of gene flow and migration studies are also discussed.