The Modern Evolutionary Synthesis relegated the ontogenetic development to a “black box”. In this article, we argue that the absence of ontogenetic development in the Evolutionary Synthesis was due its strong foundation in transmission genetics. We discuss three research strategies of transmission genetics that created an incompatibility with the ontogenetic development: (i) particulate inheritance model; (ii) population as locus for genetics research; (iii) and experimental tools that have been applied to remove “non-heritable fluctuations” from ontogenetic and environmental effects. These practices have contributed to the strength of the genetic inheritance, but also excluded the ontogenetic development from the explanation of heredity and evolution. This distinction has been perpetuated in the Evolutionary Synthesis.