After Fisher, Haldane and Wright’s iconic contributions to population genetics, scientists have been trying to isolate genetic from non-genetic factors and thereby understand the basis of genetic variation in populations. Identifying the phenotypes of a population to differentiate their components present challenges that are inherent to the analysis itself. Often this decomposition is inefficient and significantly influenced by environmental factors, posing major challenges for scientists. However, at the end of the 1960s, with the emergence of protein electrophoresis methods and a substantial theoretical production in population genetics, researchers were able to access genetic variation more efficiently, independent of the influence of the environment. Currently, with the most advanced DNA sequencing approaches, along with powerful computational equipment, the genetic bases of quantitative variation have become clearer, and important scientific advances have been made. In this chapter we expect the reader to understand the main concepts and applications of additive and non-additive components of variation computed from quantitative traits, using neotropical organisms as examples.